Negotiated link speed considerations for SSD choice?
Think of it as the chain is only as strong as its weakest link.

Yes, there is. You need to look at the specs on the speed of each of your drives. Check in the About this Mac in your toolbar and go to more info, System report, the the sata section under Hardware. 

In terms of the optical and main drive bay's, it doesn't matter which you use if both are capable of the same speeds. In most cases dealing with older models, the traditional hard drive bay provides the better speeds than the optical. I've read before that the optical bay will not always match the traditional bay.

I'd put my SSD in the main bay and your secondary drive in the optical. You can configure which drive to boot from within System Preferences if you choose otherwise.

I'd def put my OS and your applications on the fastest drive and use that to boot from. If you are using a regular hard drive to place in either of the bays then I'd also recommend you put all you media and other large less accessed files on that (especially if storage space is a concern or for some reason you are concerned about read/writes on your SSD).