I use Macromedia Homesite Text Editor mainly cuz I like the color coding, and....
I have my own little rules about including, and that is if I am doing dynamic stuff (db stuff, etc...) I will usually include that since it is most likely gonna be on more than one page.
I also like to use the common Header/Nav/Footer includes, if the site is gonna get over 10 pages, otherwise a search and replace will suffice for me if its less, when it gets over that I will almost always use the includes.
Another note, I include all connection pages, just cuz it's simple enough to do and you don't have to track down a connection problem cuz you forgot to put it into the page.
Along with that, I generally get the site ready, cut it up and lay it out in homesite, when I have all the nav, graphics, etc... I will save that out as template.php and then I always have a nice clean page to start with.
Oh and btw, I don't care for Dreamweaver's templates, all it really is, is a glorified include, called .dwt.
my 2 cents... // have 4 cents left now