Whether you run one site or several, there are some basic things you should do right now. Here's what I do right off the bat; the advantage to doing it in the "root" database is that when I make copies for my other sites this has already been done. I'd give you a link to something on the Drupal site, but I never found anything like this.
Administer>>User management>>Rolesand create an "administrator" role.
Administer>>User management>>Usersand create a user entry for yourself. This allows you to test the site by changing your role to meet your needs.
Administer>>User management>>Access controland allow the "administrator" role to do everything.
Administer>>Site configuration>>Site information>>Anonymous user) to "Visitor." As long as you're on this page, set basic defaults for the other fields.
Administer>>Site building>>Modules). For example, you will probably use "Page" on all sites, and maybe "Story." I am finding more and more uses for "Book."
I do recommend turning on (enabling) the "Path" core module so you can use "normal" names for your pages.
There are a few things I recommend that you do in all your databases, so this is a good time to do it:
Administer>>Site configuration>>Clean URLs. At the bottom of the verbiage there is a link to run the "Clean URLs Test." If it passes, then the "Enable" radio button will un-dim. Click on that.
Administer>>Site configuration>>Input formatsand set "Full HTML" as the default until I get the site ready to go live. Then I still allow administrators (like my other ID) to use that format. Do this now and you will avoid a very common problem with building your site.
Administer>>Content management>>Content typesand turn that off - in each format.
Administer>>Content management>>Post settingsin Drupal 6) and set the comments to be entered on a "separate page" and make sure that "Preview comment" is set to "Required."
Administer>>Site building>>Menusand locate the "Contact" item. Click on the "enable" link. Remember that later on you will want to go to
Administer>>Site building>>Contact formand finish setting that up.