I don't understand, I thought I could configure Isboxer to log in for me but I haven't found anything on passwords
There are no current plans for ISBoxer to enter your passwords for you. There's no secure method for automatically entering your password for you, and even if there was it'd be different in every game because there's no real incentive for a standard.
What ISBoxer CAN do is help the game store/access information separately per character. For example, most games will store the last account that you used in some file, so ISBoxer can help keep a different copy of that file per account, so you don't have to enter the right account name each time ISBoxer launches a character.
It does NOT otherwise change the login process at all. Any interaction you had to do to log in beyond what the game was designed to store, you still have to do.
or even an understanding of how it would pull up two clients and log in for me.
Well, since you didn't mention the game you're playing I can't give you any game-specific tips or do any testing. So here's some information that may or may not help.
First I'll give you an understanding of how it would pull up two clients. The way it works is when you launch your ISBoxer Character Set it will launch the first game instance. Once the first game window is up (not a patcher) with Inner Space working properly (FPS indicator) and ISBoxer also working properly within that, ISBoxer will launch the next game instance. Whether this particular process works or not
typically depends on the game and whether Inner Space and ISBoxer are working correctly with it.
One common reason why it would only launch a single window is if you specifically launched a single window instead of launching your team -- sometimes when I help people through the "it only launches one" issue it turns out they selected (for example) "World of Warcraft Default Profile" from the "World of Warcraft" submenu in the IS menu. Doing that would simply launch one instance of the game and completely disregard any configuration you did through ISBoxer, whereas selecting your team from the "ISBoxer Character Sets" submenu in the IS menu will correctly launch your team.
There are lots of fixes in the dev build of Inner Space that may or may not help with whichever game you're playing.
Rift and Earthrise betas for sure. To try the dev build, right click the IS icon in the system tray (notification area) and select Patcher, check "Download development (test) patches" then close and restart Inner Space.
Also, the Quick Start Guide is one of the most helpful resources for new users:
http://isboxer.com/wiki/Quick_Start_Guide (it doesn't go into any detail about this issue)