There are a couple of different approaches for fills, both the "traditional" fill as well as the "live paint" option if you have a newer version of Illustrator. Which version do you have? What I do for semi-complex fills (like water areas) is to copy all of the appropriate lines to a new layer, align them properly, change the stroke to 0 pt, and make a "live paint group" of it. Once you close any gaps, you can then use the live paint tool like a paint bucket.
For the Join command (ctrl J) to work properly, you need to make sure you've only selected the two anchor points at the end of each line that should be joined. This means you need to use the "direct selection tool," which is the white arrow just below the black arrow ("selection tool") you normally use. Make sure you only grab the two end points and you should be good to go. As an alternative to having to always Join wall lines, if you have "edit selected paths" checked on the options panel for the pencil tool, you can continue the lines you've already drawn by starting to extend them with the pencil tool while selected.
That's kind of hard to explain in a forum, but Brandon Kowallis has an excellent video tutorial that demonstrates it (which is how I discovered this). I BELIEVE this is the proper one:
http://www.brandonkowallis.com/Resource ... gWalls.htmIf you want to send me the file, I'll take a look and try to help. Monsieur Lovaas will surely disclose my email address for a nominal fee.
"Although it pains me to say it, in this case Jeff is right. Plan accordingly." --Andy Armstrong