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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.

I think Wayne Leupold has something on playing 18th century lit, and I think I own it, even. But I can't vouch for how good it is. The standard historical document -- at least to my mind -- is C.P.E. Bach's Essay on the True Art of Playing Keyboard Instruments.

I think you can buy mats for drum sets that are supposed to insulate the sound? Honestly, you might be just as well off with those kids’ foam play mats that link together. Ex. https://www.amazon.ca/gp/aw/d/B001HDCIIQ/ref=mh_s9_acsd_top_b52wluF_c_x_5_w?pf_rd_m=A3DWYIK6Y9EEQB&pf_rd_s=mobile-hybrid-3&pf_rd_r=676HVPVAGZ4PFE549MPM&pf_rd_t=30901&pf_rd_p=11e8e8a1-58f9-5e9f-9470-824e799fa7b1&pf_rd_i=4624224011

http://www.wayneleupold.com/first-organ-book.html

"First Organ Book" covers the techniques you'll need transitioning from piano to organ (including pedals). Another one is "Pedal Mastery" which also includes trios.

https://www.amazon.com/Pedal-Mastery-Organ-Joyce-Jones/dp/0769250440

Having an instructor can be very handy to make sure you don't develop bad habits from the start. Also, they can make it a lot easier to learn about organ controls and registration.

Well maybe you can find it as a PDF. :) I don't expect anyone to pay $200 for it!

Method of Organ Playing (8th Edition) https://www.amazon.com/dp/0132075318/ref=cm_sw_r_cp_apa_i_02pWCb54GXJVR

You're exactly right, just as choirmasters don't stop to think about what voice types to use in a piece; for the aforementioned two Masses, the composers would have heard boy sopranos and altos, not female sopranos and mezzos, or countertenors (the French really hated countertenors and castrati!). In addition, the text to these Masses would have been sung according to the local Latin pronunciation (e.g. the Italian "Sanctus" v. the French "Sanctys", in IPA), which was widespread until recordings became universally available around the late 1940s. The conductors interested in historical performance practice always overlook these things for some odd reason, when (I think) it's of paramount importance to the affect and tone color of the piece! Anyway, sorry, rant over.

To answer your question, the most (and maybe a bit too) thorough guide is by Peter Williams: The European Organ. It only goes through 1850, but the detail is absolutely amazing. It's the textbook of Organ History and Design classes in nearly every university.

Find a music teacher who can teach theory would be the best bet.

One book that I used when learning counterpoint with my teacher is "Elements of 18th Century Counterpoint"

https://www.amazon.ca/Elements-Century-Counterpoint-William-Andrews/dp/0769277713

The folks at the college I attended used the John Stainer organ method book for their organ lessons. It doesn't cover how to turn on the organ (usually a key turns or there is a switch!), but will help you get over the bump of adding pedal work and adjusting your touch to the instrument.

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

This is from what is probably my favorite organ recording of all time.

Gerre Hancock wrote a handbook called Improvising: How to Master the Art. I have it, but haven't started working with it yet.

this is a great book: http://www.amazon.com/gp/product/0570013267/ref=oh_aui_detailpage_o05_s00?ie=UTF8&psc=1