What is the best way to protect bare metal repairs to previously rusted areas that will allow me to primer and paint over later? Should I be using a primer on bare metal? If I use a rust preventative spray paint like rustoleum or rust encapsulater can I prime and paint over that later? Just looking for a little advice as I'm not a paint guy. Thanks in advance.

If you're painting over bare metal you should use a self etching primer that will bond to the metal much better.

Your best product would be epoxy.
Buzz it with a DA & 80 gt. the bare metal,clean with grease & wax remover with clean white rags until it wipes clean,shoot 1-2 coats of epoxy on and your sealed. Any "primer" be it etch or 2K will absorb moisture and eventually start rusting.
If your just wanting something "temporary",the enamel spray can will work but be sure to remove it all before proceeding later. Some still use etch primer but most resto guys are all using epoxy now. It's just a better product and it's WAY easier to use now days and will seal the metal from any further moisture issues.You can apply filler directly to it as well and some are using only epoxy as their paint base. Excellent on fiberglass.

Thanks for the info guys. 85, do you know of any specific epoxy products that work well?

PPG's DPLF 90 is what I use.

I agree with the epoxy recommendation.
I'd get the Omni line of epoxy from PPG. I bought DP40LF from one supplier. I found a supplier much closer to home. He said I can use DP40LF or the Omni line which is virtually the same product. I can't remember the PPG number it was either MAP 175 or MAE 175. I sprayed the Omni next to, over, and around the DP40LF and can't tell the difference other than at the cash register.

I use SPI as of late. Their products are second to none.
The epoxy sands like primer and is VERY user friendly.
I order from Baker PBE out of Georgia and it's generally a 2 day deal and the shipping is VERY reasonable.
The PPG is great stuff also but PPG in my area is too high in price. I mainly used Dupont Nason before but the SPI products are just outstanding.