It all depends on the organ, and tone. Recording flat is the best policy. But I find on a lot of my vintage equipment, that a cut in the 800hz-1khz range works well (using Parametric with a Q of about 1.0-1.5). This gives a little more room for the upper bass guitar or lower-mid guitar range to work. If an organ sound is real bass heavy, I'll roll it off between 75hz-250hz (75hz with bass oriented tones like 16' or 32' organ tones, towards 250hz with tones that can support itself with a broader upper spectrum like 2', 4', or 8' type organ settings). But these are just general guidelines, by which I often mix. It ultimately comes down to how you've mixed everything else. But I find if I write a song around organs these are good starting points.
