Depending on which kit you used....... it may have wire numbers/labels printed on the wire etc...... It doesn't matter where you cut the main pwr wire to the window switches. My windows relays are located behind my dvr's kick panel. The only place I do not recommend, is inside the door it's self....... unless you can waterproof the relay connection.
If you are comfortable with wiring etc....... pull the fuse block apart and see if you can re-route the feed for your window fuse. ie.... right now it's on the constant 12v buss you might be able to cut it off the constant buss and put in a jumper to the switched/assy buss.
If your wiring kit is from a major player, they often have provisions for installing a relay directly to the side of the fuse blk....... it would be very easy to locate the window pwr out wire and cut it right at the fuse blk, hook it to the relay etc.......