Cockpit Tent:
Another idea I discovered on my own (standard disclaimer, others may have discovered before)

Instead of sewing your own cockpit tent, just buy a regular camping tent and cut the bottom out of it, install some snaps and affix it to your boat. I used this concept in my 2000 Duckworks boat design contest:

http://www.shortypen.com/boats/shorty14/
http://www.shortypen.com/boats/shorty14/entry.gif