The better rustproofing systems I found using the stuff almost daily back in the mid 80's were runny and sticky as PG13ery so that they could get into almost anywhere - and stay there. The system we used where I worked (can't think of the name of it but came in two or three black tins - thinking about it, it may have been Endrust but thinbk there were two ro three ones in use back then) involved a darker spray that was applied under the car and a light fawn coloured one that did the doors and other hard to reach places.

A one inch piece of a Maccas straw (or any other stiff straw that will hold its shape reasonably well) inserted before application into the drain holes of the doors and tailgate etc will stop the holes clogging while the material begins to solidify after the few hours/next few days. If you leave about 5-10mm of straw protruding from the bottom of the holes you can pull them out later using either fingers or pliers. Should you find you end-up with a blocked drain hole it is quite simple just to work a bit of wire or even a small flat blade screwdriver up into the holes to clear them.

Regards,

Dave.