I started with a Mighty Mite Neck (CR2910) which has a rosewood finish on the fretboard - however, it really didn't look that great and I was using a black pickguard which made the flaws in the rosewood show even more. The difference in the finish product is night and day - it really looks much nicer, and didn't take much effort at all.
Note: It's important that the NON-FRETBOARD part of the neck has some sort of finish on it. Don't use this method on a raw neck.
Step 1: Preparation
Once you have that done, wipe down the neck with odorless mineral spirits. I would recommend wearing latex gloves in order to prevent leaving any fingerprints on the surfaces you want to stain.
Step 2: Taping up the neck
Step 3: Staining
Really lay the stain on there, over the fretboard, the nut and the dots (you can tidy those up later with mineral spirits and a q-tip, and it won't stick to your frets at all). Once you have it on there, leave it alone for at least 10 minutes. The longer it's on there, the darker your finish will be.
(I think anything past 30 minutes is a waste - dark only gets so dark...)
Step 4: Finishing the job.
Use a piece of cloth (I used an old t-shirt), rub off all of the remaining dye. When you think you are done, put the neck down and wait for a few minutes, then do it again with a clean piece of cloth. Repeat this step until the cloth comes up clean. If you think the fretboard isn't dark enough, apply more stain and wait another 10 - 30 minutes, then wipe the stuff off.
Once it's "dry," you can now remove the tape. You will notice that some of the stain has bleed under the tape (it's unavoidable), but it's easy to clean that up using mineral spirits and some paper towel
Let the fret dry at least 8 hours (overnight is good). If you need to tidy up the dots or nut, wait until this drying phase is done.
Thats it! A nice deep dark finish on your fretboard!