well, it doesnt really matter, sort of.
you can boot from either, and it will automatically know/choose the osx boot drive. so it doesnt matter where you put it, but....
the only thing that would matter is the speed. as in, will having the ssd in the optibay have a slower connection then it being in the main drive spot. since your ssd is 3gb/s (sata II) then, maybe it wont matter since i believe they are both sata II connections. however, you say the optibay is pata so its not going to work in the 08 macbook pro. if you get a sata optibay, both spots are basically the same. (if both do sata II) my 09 has sata ii in both bays.
however, i have seen threads here about issues with SSDs in optical drive bays. but on the other hand, theres been issues with SSDs period. so who knows.
if it were me, i would put the ssd in the main drive and the hdd in the otpibay. just because, its not a brand new machine, so go ahead and dig right in. however, with that said, im getting a new 2012 non-retina macbook pro delivered tomorrow which will have a 750gb 7200rpm drive. i will put a ssd in a optibay for osx. im only doing it this way because its a brand new computer, and i dont want to accidently screw anything up right now. (but i have done it in several other unibody macbook pros, but they were refurbed or old, so i didnt care about digging in.) but i may switch them arround in a few months or after the first year.
if youve done it before, or your tech savy.....just put the ssd in the main drive bay.....i mean if your techy, then you enjoy taking crap apart anyways.....right.
edit- i dont know if the optibays connection restricts the speed in anyway either. i actually forgot about this question. i emailed them and asked several weeks ago. never heard back. i emailed them because the question popped into my head one day while i was drooling over the 2012 releases or rather, drooling because i was going brain dead from waiting for the 2012 releases....haha