I've never drilled through the Envirotex. I imagine it could be done without issue, but regardless I'd drill the holes first. Like drventure said, you could tape off the holes pretty easily. You would use the Automotive painter's tape (I believe that's the Green tape, not the blue painter's tape) and you'd tape around the hole so that the tape creates a wall around the hole. Picture sticking a TP or paper towel tube standing up in the hole. You would also want to do this around the edges of the entire CP. Sure, you'll get run off and drips, but you'll want to contain as much as possible. Don't wait too long to remove the tape afterwards.
When you pour the stuff, it's pretty thick, almost honey like. So, you'll need to spread it with foam brushes. By doing so, you can kinda control how much makes it to the edge, to the holes etc.
The covering is important, but do not let it touch the product after the pour. If you're going to do this, be sure to set something up (tent-like) and do a dry run of covering it (without dropping the cover on the CP).
I'd suggest that you call Envirtotex support with any questions. They are very helpful and might have strong feeling about cutting aftet hardening. The person you would speak to uses the stuff all the time for testing and they should be able to answer all of your questions.
Also, I don't remember the exact timeframe, but they say it takes quite some time to 'fully harden'. Something like weeks if I'm not mistaken. What I mean by fully harden is that you don't want to place heavy objects on a surface treated with Envirotex or it will leave footprints. Even though you wouldn't be placing anything heavy, mounting controls would fall into that category. If you are going to go with the pour on, speak to support and they can give you more detail.
On a personal note, for the cost and high maintenance when applying, I might suggest just doing multiple coats of poly.