Add silicone to nylon before or after sewing channels?

Stupid question, because I think the channels would stick shut from the silicone, but I figure I'd ask.

I want to make a bright red pack cover for when it rains. I have the nylon, and want to waterproof it. I heard gas stinks so I was going to use mineral spirits and clear silicone and dunk the fabric. I was just wondering if I can do it after everything is sewn or if the channel for the shock cord will just seal up from the silicone?

Thanks!