Simple question and probably has a very simple answer. If I get a separate amp (Emotiva maybe) and use my Yamaha 657 as a Pre / Pro, where do I hook the sub? Do I use the 6/7 channel on the amp or do I leave it hooked to the Yammie? Are these both options or does the amp hookup shut down any use of the Yammie? I knew it was simple.....

You will be using the sub out on the Yamaha.

As Rick has mentioned, most receivers should have pre-out RCA hookup for the sub. Normally it is located next to the other pre-out rca connections you would use to hook your other speakers to an external amp.

I just wasn't sure if I left the sub hooked where it was or if it also went to the amp like the other speakers. Ya'll answered my question. Thanks for the help.

Charles, as Rick and Randy indicated, you'd leave the wiring for the sub the same as it is now. You're now using the 657 as a pre-pro to drive the internal sub amp and that doesn't change. You wouldn't use an amp to drive an amp.