I have a base that is painted black with Industrial grade Enamel paint. This base is really more of a dolly, and as such it takes a pounding. I was going to cover it with spar varnish, and then I realized that covering an enamel piece with a water base varnish might not be a great idea. Can anyone offer experience and/or suggestions?

It could be either an oven baked enamel or cold cure enamel.
I'm not sure what is available in the U.S. but over here in the U.K. cold cure enamel is available in spray cans and is easy to apply.All you have to make sure of is that the area to be treated is de-greased(thinners,sugar soap,etc)and well keyed.If you sand down the substrate with 220 grade sandpaper prior to the first coat and 320 grade inbetween each coat,you should be o.k.
A couple of coats should be adequate.
You can also spray a little bit of the enamel onto a sheet of paper and apply it with an artists brush,should you need to touch-up any small localised damage.
Hope this helps!
Cheers,Ray.