Best practices for very long piece

The piece I'm currently working on will be 40-50 minutes long, written for a chamber ensemble of about 20 instruments. I am wondering what best practices/tips there might be for managing this project, Sonar-wise. To keep file sizes small and my brain organized, I'm creating separate files for each section, most averaging 1-3 minutes in length. Most of these sections will overlap by a bar or two, however. (For example, while the piano holds a long chord to end Section 4, the clarinet that opens Section 5 starts up.) One of the features of this piece is that there are no breaks, everything all flows together. But I'm pretty sure I don't want a single Sonar project that's 50 minutes long and 20 instruments.
 
1. I assume simply writing down slider levels and making use of FX chains is the best way to ensure the instruments sound consistent between tracks, but is there some slicker way? What if, in section 4, I've decided the clarinet is too loud, and I want to bring it down. Then I really should adjust all the clarinets in all the other projects, ugh. Anything I'm missing that could make things easier?
2. To do the overlaps between sections, I'm exporting each project as audio, then creating another project consisting of these audio exports, and overlapping these appropriately, then exporting that new project as a single audio file. Is there a better way?
 
Any tips? How would you go about this? I'm only 10 minutes into this piece so far, so I can change methods, but it's not like I haven't already done a lot of work on it.

Are you recording live instruments? I've done some long recordings just fine. Just make sure you play safe with the levels, buffer size and reboot the computer first and close any processes that aren't necessary just to mitigate the chance of something technical going wrong. You want to avoid that embarrassing walk of shame from the control room to the live room, waving your arms about, shouting, "Hold it hold it!" 49 minutes in. Then having to explain that something dropped out, froze, crashed, peaked etc. I don't remember ever having a problem like this during a long take though. Although of course, I have joked about it after the performance. "Sorry, blew the levels 15 seconds into the intro. We'll have to go again." Or even, "Sorry was that supposed to be a take? I was just doing levels. I didn't record it." Just to see their faces :)

I'm with Rob. It seems unhelpful, to say the least, to split the piece up front. I've never had a problem with pieces that long or with that many instruments (e.g. live recordings of bands and then editing, overdubbing etc.). Just make good use of markers.

Thanks everyone. I knew I forgot something. These are all EastWest sampled instruments, for now. A few will be live players down the line (a favorite trick: insert 1 or 2 live players into a synth ensemble to make the whole thing sound live!). I guess another reason for keeping it chopped up was to be able to export versions and hear them away from the computer to take notes.
 
I'm surprised the vast majority of you are saying to keep it all as one huge file, but I admit that does sound appealing. I think I'm worried about navigation mostly. Markers are such a limited feature. I would want to use them both to mark whole sections, and I also use them when I'm scoring a bunch of instruments over a complex chord progression, I make a marker for each chord change. I wish they'd give us multiple levels of markers for that. 

I like that idea of using dummy midi tracks.

But I don't really understand why you would need markers for every chord in a progression. Would it maybe be enough to mark the beginning and end and then use a dummy midi track with the actual chords and when they change?

Ha! By "note", you didn't mean notes, you meant NOTES. I thought you were talking about notes as in "make a note of that", but you meant notes that are played on, say, a flugelhorn. 
 
Still, it's a potentially useful idea. I can think immediately of having a muted track, then recording to it when auditioning a version of a piece, plopping down a note every time I hear something that needs fixing.

Phenaste
 
For the chord progression, simply use a dummy track that will contains multiple clips with no event inside, and named each clip with your chords. 

 Since I spend a majority of time in PRV, I don't think this solution is going to work out.
 

Phenaste
If you mix multiple instruments for the same stave, you can group them into a folder to organize your 20 instruments with a sub-level.

I already do that, and in fact I will open PRV for a section, then lock it, open another section, lock that, etc., so I have a tab for each section's PRV. If I could name or save those PRV configurations it would be even better, but this works good enough.

OK, thank you everyone! I have a working solution now, based on suggestions here. Glad I asked.
 
I have created a muted dummy track at the top of the project (Track 1), and entered a single Midi note at the beginning of each section. Each Midi note in this track resides in its own clip. I then drag each clip out to the end of its section, name it for that section, and give it a distinct color. Now, I can easily see each section from that dummy track's colored and named clips, and can scoot forward and backward by section with the Tab/Shift-Tab keys. Works great! What's also great about this solution is that I'm not using Markers at all to mark sections, so am free to continue to use Markers for individual cues within sections. 
 
So OK, I'm going to next combine all my separate projects into one big file. In this case, I'm trusting all of you that I'm not going to massively regret that decision :-).

jkoseattle
New problem:
 
I have to do a lot of vertical scrolling because of the number of instruments. So the dummy track with the section clips scrolls off the page a lot. To solve that, I decided to make a clone of the dummy track and place it near the bottom so that I can always see dummy section clips no matter where I am.
 
I selected my dummy track, right-clicked and chose Clone Track. In the Clone Track dialog I checked "Link to Original Clips", but nothing is actually linked. It just makes a copy of the track. I tried entering new notes, dragging clips around, clearly they aren't linked. Plus, the supposedly linked clips don't have that border around them.
 
I then tried simply creating a second dummy track, (not cloning) and copying clips individually, indicating they should be linked. This also doesn't create a linked clip, so it seems that the problem is with linking itself. Why aren't my copied clips linking? Am I missing something? 

Maybe Track Folders will help with the vertical scrolling?
If you're using a lot of MIDI tracks to feed a few Synths, perhaps create a Track Folder for each major section of the project, and in each folder create a MIDI track that only submits data for that section.
You can have multiple MIDI tracks feeding the same Synth/Channel...

jkoseattle
Thanks, I have one Midi track for one synth, not sure of a use case where I'd have multiple tracks feeding a single synth.
 
I do use track folders, but I'm scanning up and down between sections so much that I just leave them open all the time. I use them mostly for muting and soloing, and also for selecting tracks to see in PRV.

For a stripped down example, you've got 3 musical sections (verse, chorus, bridge, for eg) to the project, with a trumpet, double bass, and violin playing throughout.  
Create a Track Folder for Verse, with 3 MIDI tracks in it.  Trumpet Verse, Bass Verse, and Violin Verse.
Create another Track Folder for Chorus, clone the Verse 3 MIDI tracks, change the names, and put them in the Chorus Folder:  Trumpet Chorus, Bass Chorus, and Violin Chorus.
Create a third Track Folder for Bridge, clone the Verse 3 MIDI tracks, change the names, and put them in the Bridge Folder:  Trumpet Bridge, Bass Bridge, and Violin Bridge.
All MIDI tracks route to the synth you're using to create the sounds (all MIDI Trumpet tracks have identical settings, feeding the same channel, etc), and the Synth Outs don't need to be in these track folders.
 
When you're programming the first part, you can close Track Folders B & C, and have all the MIDI tracks visible for the first part.  Then, when you move on to the 2nd part, you close Track Folder A and open Track Folder B.  Again, all MIDI tracks are visible.  All instruments will keep playing as programmed, but you're able to focus visually on the places you're working on.
 
Does that make sense?  
It's obviously not needed for a simple 3-part, 3 instrument project, but if you're getting overwhelmed with lots of tracks and parts, it should help to organize it.
 

That's a good idea. What about working with things like the FX Bin? Doesn't that mean I have to duplicate efforts to make sure all the tracks that point to the same synth are configured the same way?