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No it does not hurt to put the drive on different ports. You say there is no option to make changes in the BIOS. Not sure what you mean there. But there should be an option in the BIOS to change the boot order. This is to ensure the correct drive is touched first. If you are booting to the correct drive, then no problem.
If you never use more than 200GB, the only thing you are hurting by getting a 1TB or 500GB is, maybe, your wallet.
Actually, that's your third - or maybe fourth! 
Umm, I think WD Dashboard is for SSDs.
By default, DMA on HDs should already be enabled. Not sure what the none means but the other values suggest it is enable.
Bottom line, is you system working? If it ain't broke, don't fix it! Windows really does know what it is doing.
