It's good that you are eager to learn fingerstyle technique because it will make you a more versatile player. I know it may seem uncomfortable now, but it's worth it.
Plucking the strings near, and even over the fingerboard will give a much fuller, warmer sound than plucking near the bridge. I anchor my thumb over the neck pickup most of the time on a J bass without much problem. I may sometimes rest the side of the thumb directly on the body to hit the E string, but mostly it's on the pickup. Yes, even though it doesn't feel right you should just get used to it and find something comfortable that gives the tone you want.
I've been playing for many years and only use two fingers, but start with one and go from there. There are different two finger techniques regarding how the fingers alternate when changing strings. I just do what feels right,

but if your intention is to play really fast you should start off right so you don't develop bad habits.
Rembember that a big part of the sound of your bass is in your fingers!! Use them wisely.
Good luck