Reddit mentions of The Organists' Manual: Technical Studies & Selected Compositions for the Organ

The best way would be to take lessons with somebody. I'd say check some local churches, see if they have an organ, and see if they have an organist who gives lessons.

In terms of technique, you can certainly develop your keyboard skills on a piano, even if you ultimately want to play the organ more. In fact, practicing hand parts of organ music alone on the piano can be better than practicing on the organ since the action is so much heavier on a piano. So, if you happen to own a piano or even a cheap keyboard you can start to practice scales and whatnot.

EDIT: But of course, when practicing organ parts on a piano DO NOT use the sustain pedal, as an organ has no such thing. If you want a note to keep sounding you have to keep holding it.

Also, The Organist's Manual is a great book of exercises and short pieces, plus some technical information about the organ.

The Organist's Manual by Roger E. Davis is considered the holy grail of organ-playing at my university. Just about every student has their own, since it has a really solid selection of pieces with and without pedal, and entire chapters dedicated to how to practice with feet and hands (Separate and together). It also has very technical and useful appendices on how the instrument works and how stops differ. Couldn't recommend the book enough.

Aside from that, it's just a matter of finding out how you learn on organ. Some do hands and feet separate, and some just tackle music all at once (hands+pedal). CrownStarr's comment on expression and registration is spot-on too - I'd recommend finding as many different recordings online as possible once you get a feel for what kind of pieces you like. There's a massive difference in style/registration between, say, Biggs/Alain/Richter.

My instructor has me play from the Davies Organists' Manual.