Well, here's how I got into it....
When I studied classical, I played the Bach 2 part inventions. The process that I went thru to learn those pieces I apply to playing organ-which is:
Play each hand separately for about a week. As you get used to this it won't take as long. Use a metronone, on quarter notes, eighths if you have to. Start slowly, and master it before you increase the speed.
During this time develop consistent fingering for each hand. If you're reading music, mark the fingerings. That way you can let each hand go when you put it together.
After this time, start putting the hands together, slowly, with the metronome. When you get confident back off the metronome to 1/2 notes, or even whole notes, so you're only giving yourself the 1st beat of each measure. This will help you start grooving with it, and will keep it from sounding too mechanical.
Drop problematic sections back to one hand at a time.
Practice scales everyday. One key a month will get you through them all in a year. I'll be happy to post scale fingerings for all the keys if they aren't already available on this site. There are different kinds of fingerings for the scales, pick one and stick with it.