dannyjmusic
U less I'm missing something
12/8 is the same as 4/4 with an 8th triplet on every beat. You would just make sure the triplet 8th notes are the same tempo as the 8th notes in the 12/8 bar
It's really just how you count them in you head
The feel is basically the same

No, you are right. It's just that in 12/8, you don't need triplets. Three 1/8 notes in 12/8=One Triplet group in 4/4. As sonar tends to have problems with tuplets, I sometimes go with the 12/8 if I have extended periods with 1/8 note triplets. On the other hand, in 12/8 you will sometimes have to use duplets for double 1/8 note figures. Just depends on which way you would have more tuplets (tuplets being the generic term for duplets, tuplets, quadruplets, etc).

I would go the route Bapu mentioned as well, but made me wonder if you can get away with freezing synths in a project (so no "MIDI" is exposed - only audio) and then change the time signature on the entire project and work the other part "in place." I have honestly never tried this, so not sure if it is a feasible option (i.e., not sure how that frozen track would react to a signature change).

I'm just thinking out loud here, but what would happen if you set the time sig to 12/8 - record all those passages then change it to 4/4 for those bits? All in Midi I mean. Would it totally screw the timing up?
 
 

If you position lock the data I think it should work.

Sanderxpander
If you position lock the data I think it should work.

MIDI clips "lock" does not fix absolute time for events. Events are timed in ticks, so in M:B:T domain and so changing the tempo still influence locked MIDI.
 
The method I have mentioned before recalculates event positions in one tempo (signature) to another using absolute time. It calculates absolute time for every note in the original (for that clip) tempo/signature and map the result to the current tempo/signature. The first part is what happens during rendering MIDI into audio, but the second conversion is what allows to keep the result in MIDI format.

Ah thanks for clearing that up.