It's pretty basic, you take out all the parts having to do with the automatic, and put in all the parts that have to do with the 5 speed. Only place I ran into problems was with the wiring for the IACV on the intake manifold, and the brake pedal, wich needs to be replaced with one from and 5speed so it won't hit the clutch, although it might be different for 5th gens, I suggest going to a junk yard and finding out. Or try:
http://www.hondaautomotiveparts.com/
and start comparing part numbers between the auto and 5-speed.
That's what I did.
Oh and don't forget, Please oh please get a 5-speed ECU.
As for steps, get a Helms manual for your year and follow the instructions for removing the auto and go to section for the 5-speed for your year and follow it to put the 5-speed in.