If you are using onboard RAID adapters, I doubt it will make a difference, as far as recognizing the ARRAYs.
If you are using hardware RAID cards, then you could run into some issues there.
I know on my system at home, I had installed 2 SATA hardware RAID cards with no problem (onboard RAID disabled, of course), and had no problems. Then I tried one PATA RAID card with no problems - but for what I was wanting to do it was not efficient. So, I got another PATA RAID card. Now, with this one, I couldn't get the system to boot. So, for now I just took that out, and laid it to the side, skipping the use of it.
What I'm trying to say with that example is that I would suppose that you'll have no problems, or you'll have one of these (but it all depends upon how well the hardware plays together):
1. System won't boot at all.
2. System will recognize likely the 1st RAID card only, if it will only recognize one or the other.
3. System will attempt to boot, but not recongnize either RAID Arrays.
Hopefully that helps your thought process a little, instead of muddying it.
--
"If to err is human, then I must be some kind of human!" -Me