Glad you are going with the overlap. That's my preference.
I know that some find it easier to fill the weave in glass with some fairing compound mixed into the epoxy, but I generally don't ... but I also don't use heavier than about 10-oz as a last layer of glass, so the weave doesn't need a lot of filling. What I do is to first sand the cured glass lightly with a random orbital and around 100-grit paper - but lightly, just enough to smooth the epoxy a tad without getting into the glass. If you DO touch a bit of glass here and there, don't worry about it, just try not to. I find that with a light sanding like that, that the weave will fill much easier with straight epoxy rolled on. That said, I do know that some swear by using some fairing compound - I just haven't found it necessary myself yet.
And yes, it's OK to fill the weave before you add the side glass, and I do recommend it to some degree ... noting that you don't need to work so hard on it that the weave is finished completely. After adding the side glass, you'll need to do similar work anyway. Just fill enough of the weave for the next layer of glass to lay on it smoothly and call it good. Do your 'finish work' later.
Brian