We are in the process of finishing our basement. I am doing all the work, except for the HVAC......I would like to rough in the ductwork now and later on have someone install the furnace and a/c unit....Anyone ever done this? Is there a good website to give me a good starting point as to how many and where I should place my registers and returns?

you are putting in a whole new system for you basment?

Unfortunately, you're approaching this from the wrong direction. To properly install an HVAC system you need to first size the system for the dwelling, then given the blower CFM you size the ductwork.

So if you have a system spec'ed out already you could put in the ductwork but there are many tricks to getting it right. To learn more get a copy of Manual D and you will understand how complex a proper ductwork setup can be.