I too use my own css. I used bootstrap before, but I wanted more autonomy on my design .
As I modified classes, it started to get messy. I isolated classes I wanted and added extra css properties, but had to leave all the bootstrap css there (version I downloaded).
So, alot of superfluous classes are unused. It can affect inheritance too if you really want to customize your design.
So I use my own css. I also break up my css into separate files that are relevant for sections of my projects.