Adding internal hd - stock drive?

I've been reading a lot of posts about hard drives, but haven't found this answer.
When I buy my Mac Pro, I plan to buy and install a 500G hard drive for use as my main boot drive. The 250G stock drive, I plan to use for Win XP/bootcamp. I know I can set which Mac is the start up drive, but, if I am ever having problems, will the OS try to boot from bay 1 before trying others? Is there a certain bay order the Mac uses to search for a boot volume? If there is, then this will effect my startup time. Should I move the stock drive to bay 2 since it won't be my main boot drive?
I plan to really test the new Mac for at least a day before I erase the drive and continue with installing anything permanently. So, if the drive needs to be moved, I'd rather do so at the onstart. I'll have to open it up to install the extra RAM anyhow - after testing. I want to be able to observe the difference between the stock and additional RAM. I didn't do this with my PB, I just made sure it wasn't DOA for an hour, then erased.

Already covered on the backups. I have Firewire and USB. Next month or so, I want to add another internal drive, and then add a network drive or get a larger FW for backups by the end of summer. I learned to do frequent backups years ago because I'm surrounded by pc users who have lost their data because they failed to backup. I was against floppy drives ages before Apple stopped putting them in new systems, but know a surprising amount of people who lost data because they still think floppies are reliable for backups.
Yeah, I've installed hard drives and RAM and even graphic cards in my Macs before. Hopefully, there won't be any problems with the new Mac even though I haven't installed internally since my airport card in my PB. I've already prepared myself to force the RAM in a little from others posts in the forum. I downloaded all of Apple's DIY documents for the Mac Pro a while ago, even those for the iMac, because I wasn't sure which I'd go with. In the end, having the flexibility to upgrade the internals, and the extra USB ports won me over when I decided that I CAN afford it. (Trying to eat an live frugally until then, but it will be worth it.)

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    Hi,
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    it's an LG, "HL-DT-ST DVDRAM GSA-4120B" according to
    system profiler. I'v left the original apple
    superdrive as-is, and put this in the second bay. I'm
    pretty sure I've set it's jumpers to "slave", but it
    was in an external bay and I don't have a manual or
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    (or vice-versa).
    I was under the impression that both drives can be
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