Howdy Vec;
Yes, you can hook up your C9 distributor to a full manifold vacuum source. Ideally, this distributor would use a ported vacuum source, which would give no advance at idle, or other high vacuum situations, like steady cruise speeds. With a ported vacuum source you would ideally set your initial advance at around 12 degrees BTC with a manual trans and 16 degrees BTC with an auto trans.
In your case start by setting your initial in the 6 to 8 degrees, with a manual trans or 12 to 14 with an auto.
The negative that you ask about is that the manifold vacuum source increase advance too much at steady highway speed. Watch your plugs for signs of high chamber heat. Peppering on the porcelin or glazing. For around town driving you will miss the feel of the extra few degrees of initial advance, but that's about all.
Oh, ya, just cap off the SCV source on the carb. No need to remove it or otherwise plug it.
Good luck and keep us posted.
Adios, David