from my experience this is a problem for a big number of "key" players. there are some things that i have done to help with that problem. i played drums when i first started and then piano so i was always trying to play my chords with beat. 1) now the obvious is holding out your main chords. it will have to go with the song but you can try every key phrase of the song. i.e. can't nobody. "can't nobody do me like jesus" then play another chord for the next phrase. this is alright for when you first start to get you used to playing so on beat. 2) next what you could do is listen to some runs and stuff other organist do to get the feel of when to throw them in and how some sound like. 3) be sensitive to where to the music is going and where you could make it better. 4) know your fellow muscians and fill in on there weaknesses as they will fill in on yours. pretty basic stuff but it mostly comes through practice, practice, practice. a good organist to hear is the one who plays on carlton pearson azuza 2 precious memories. can't remember the name right now but he's tight.
god bless and good luck
enson