EVE's new Launcher, how to make it work well with ISBoxer
ISBoxer 41.2.0522.1 adds virtualization of the new EVE launcher's Cookies file which stores your Usernames, and Inner Space build 5844 corrects a minor bug with virtualizing this particular file. So, you will want to update both ISBoxer and Inner Space. Both of them should offer to patch (or automatically patch, in Inner Space's case) to the necessary versions simply by re-launching ISBoxer and Inner Space.
After updating ISBoxer, the Virtual File Wizard and the Quick Setup Wizard both include settings for setting up the virtual "Cookies" file for you. If you have existing Characters (in ISBoxer) you want to set this up for, use the Virtual File Wizard, tell it EVE Online, and pick the Characters to apply them to on the last page. Export to Inner Space after doing so!
When logging into the game via the launcher, each launcher window comes up one at a time. Make sure that in the EVE Launcher Settings, in the Startup tab, the check box labelled "Close the EVE Launcher after starting EVE Online" is checked. After you log into the launcher and click Play, the game instance from that launcher will come up, and the launcher will close. When the game instance comes up, the next launcher will automatically come up.
Finally, until CCP corrects a couple minor bugs, you will have to use a workaround in order for the Cookies file to correctly save your Username for each Character. Just logging in and clicking Play is not enough to save your Usernames! If you need to change the Username that comes up in the box, including if that box was empty when the launcher came up, you will need to log in, then click "Switch user account", and then log in again. I have mailed CCP Atropos about this issue via the EVE forums, so hopefully it gets resolved soon.
After logging in for the first time and ensuring that your username saves, you will not need to enter or select the Username any more, just your password in each Launcher.