When I do fills, I usually make sure that they are in places when people arent singing. So when there is a short pause in the singing, you can throw in something It just sounds better that way. Our job is to support the singer, not to throw in runs whenever we want.
Just like when doing runs, you have to know the the notes in the scale of the key that you are in, and you have to have good timing. When you have good timing you will effortlessly be able to land on the right note in time.
How did I learn fill ins? When I first started playing, I would listen to recordings of musicians and mimic as much as I could. That really helped me. Being able to do fills will not come over night.
So my advice for those having problems with runs and fill ins, is to count. Yes, count. Even write it out if you have to. the song usually goes 1234 1234 1234..... You can do almost whatever you want in that scale as long as you get to the 1 on time.
Listen to this clip. The organist and guitar player are mostly doing fill ins. Notice how we land on the same note as the piano player at the same time.