I'm pretty new to the world of Guitars and Amp, I've never played through a real amp, so just have TH2 (3 sort of) and MarkBass. These come with stomps of compressors. What would be the benefit of using these before and amp over those in the DAW; CA2A, PC76 and Boz+10 for example. I'm guessing having a modelled high end compressor over a modeled stomp box.
 
I've also been investigating pick ups and note comments like 'more attack, more sustain, deeper sound, more even dynamics, more presence etc. These all seem the subtle qualities you can achieve processing the sound pre Amp Sim, to mimic a better sounding an instrument. Of course a better sounding instrument would be better, but I've wondered about using transient designers, Channel eq's etc before the amp sim to achieve these qualities

Amp sims can house the entire chain which is a nice feature of their presets. The only thing I personally use prior to an amp sim is a limiter in my interface. That is just to prevent clipping inbound.

I would suggest not getting too heavy handed with compression or gain before an amp (sim). If you compress or gain signal you do not want, it is incredibly difficult to remove later.

Do you ever use the compressors stomp boxes that come with Amp sims?
 
Anything I'd try wouldn't be applied to the audio file, so it would easily be removed.
 

Compression is good prior to heavy distortion. Gain and compression feeding a distortion module will get more out.

The stock presets are a good starting point with TH2, since building a chain from scratch can be tedious.

Not so much for me, as I prefer clean. And end up trying to find out what in the stocks are causing the signal to break up. My thinking would be more to presenting a more level playing to the amp, to make up for my playing inconsistencies.  
This is for bass as well as guitar.
 

I attempted to upgrade to TH3 last week, but gave up after about 20 submissions to MyCommerce to pay for it.
 
Although I was more interested in the Bass amps and Cabs that the Guitar. Thought the options in TH3 would contrast against the modern MarkBass Tones, 

Can you clarify the signal breaking up? You mean the signal dropping out? A compressor can help some with this, but the signal will just "cut off" at a certain point. Same with using a noise gate. A feedback loop of some sort (guitar receiving the notes back from a speaker) will help sustain but can be tricky and potentially annoy others. Another option is to raise the height of pickups to be closer to the strings (fret at the highest fret and adjust the pickup height so that it almost touches). The bridge pickup is good to do this with (since it also catches more harmonics), but the neck pickup is usually best left down a little below that (depending on the output).

By breaking up, I mean distortion coming in. The stock presets in TH2 seems more for rock and blues players. So I start with a clean amp and cab, than use presets. I never seem to use presets in anything, synths. drum machines FX or anything really

Regarding pickups, I don't think you'll find stomp boxes that'll do what various pickups will do. The pickup magnetics interact with the strings and ways that are dependent on how you strike the strings. The non-linearities in the magnetic core of the pickups also modify the tone in ways that are dependent on how you strike the strings. The position of the pickups relative to the end points of the string and position of the right hand also changes how the sound transforms over time. These are all examples of dynamics being in the hands and why people have so many guitars (they have different pickups and react differently to how you play). Stomp boxes have no information about how to strike the strings. They can't react the way pickups do.

I think you've misunderstood me. I'm asking about using and engineers compressor (LA2A, 1176) instead of an amp sims stomp box. I'm also asking about using other tools and engineer would, such as transient designers, EQ such as the quad EQ, and the preciously mentioned Compressors, to condition the bass/guitar, before the amp sim, insetad of after. To introduce subtle qualities in the same way that having a different pickup would bring to an istrument. I know in the later case, it would be the same thing, but just as away to improve the tone before amping.