high top sliding windows

[jamesandtheopenroad]

So i'm trying to sort out a leak before it becomes a big problem and I have removed my sliding window in my high top to renew the seals etc and I've spied 3 drain holes on the bottom of the frame. Obviously they are supposed to be there but i'm wondering, once the frame has some back into the rubber seal with some silicone adhesive, won't they be blocked up? And if not, won't they just leak back into the van?

I'm a little confused.