Let me explain. In fl studio in both the piano roll and the playlist view every 16 beats the colours switch between grey and a lighter grey alternatively if you have a 4/4 time signature. With a lot of music though you often end up having a fill between two parts that only lasts 1 beat or 4 beats or whatever and then your whole song after that is out of sync with those coloured sections. Obviously it doesn't really matter but I've always wondered if there is a way to fix this? I would have googled it but I wouldn't know what to google really, didn't even know what to put as the title to this question.
I'm not sure if I got the question right, but here is my answer : Simply put your fill on the last beat or so of your part, so nothing is out of sync, that's what I usually do, and that's what most people I know do too. Hope this helped.