It seems to me that using a spray type covering would work better here. You can solder everything in, then spray the copper side with a varnish. This way, you wouldn't have to mess with scraping, or covering the pads before you spray. They sell cans of varnish for about $3.00, and should last quite a while (5 or 6 PCBs).
One point of consideration: I'm not sure if varnish is actually conductive in any manner, so you may want to test to see if the varnish is conductive. You can spray a layer on a scrap piece of plastic, let it dry, then see if the varnish is conductive using a continuity tester. If it conducts, the varnish idea wont work.
Another point of consideration:
I'm not sure if the varnish will react with the rosin used in solder, so you may want to make sure your board is pretty clean of rosin / flux. Otherwise, the varnish may bubble up in the areas that the rosin covers. You may get lucky, and find that these two wont react, but I think it is a worthy thing to find out. You could probably test this by taking a scrap piece of PCB, solder some drops onto the PCB, then cover with the varnish.
Good luck!