Hey again DreadStarX!
The performance shouldn't be overall affected other than your system should be able to read the hard drive with it's full capacity. But I suppose it would depend on your build as a whole. Your motherboard sounds like it could give out problems.
As I hear how you describe your situation, I'd say that you should first of all change your motherboard if it's giving you so much headaches. From there one, by choosing a better one, may be even with UEFI BIOS, your doubts and questions about the hard drives would disappear and you may even not need to use an alignment software.
Secondly, you need the big capacity HDD to store data on it, as in music etc., is that correct? I'm asking this because the WD Green are designed for back ups and archiving and perhaps wouldn't be that great in loading massive programs and such, as to their design.
Lastly, I would agree with all the others, you should be able to run a SSD on your motherboard even if SATA II, but as I said, if the motherboard's being such an issue, you should replace that first.
Just in case, the link below is on how to use the WD Alignment Tool, from the WD Knowledge Base:
How to use the Acronis Alignment Tool to realign an Advanced Format drive
Cheers and best of luck! :)
CK_WD