Hello Matt 
,
thank you for checking it out!
There are several ways to run bots in the background.
The easiest one probably is using a virtual machine. People often do this with EVE Online.
A good virtual machine software that works with Windows is Hyper-V:
Some people also use VMWare with EVE Online, another kind of virtual machine.
There is also the option to use remote desktop protocol to create separate desktops on a single system, each with their own input focus and mouse:
However, as far as I remember, using RDP in this way is not supported by Microsoft, and people resort to third-party tools like RDPWrap to make it work.
There was also this post explaining a setup with RDP: Multi instances Support - #10 by tester