One way to be able to run multiple accounts at one time on a normal system is with InnerSpace. Feel free to search it out and learn about it. The problem I can see with it is that each window has a different name, and the bot is not set up to be directed to a specific window out of 3 or so running EVE and might just get confused.
What IS is capable of is quite amazing. We used to have full blown WOW bots for all classes that ran via IS, but due to legal issues the Programmer ended allowing WOW bots and eventually all bots from his site. However, you can still find bots for various games that are made to work with IS.
I was having a damnable time with the bot not working properly, but I'm learning more each day. I like to be at my computer, so maybe what I shall do is to use it in fight mode only.