I thought about this for long. My suggestion is that you can install Everything twice and both programs have their own settings (at least index options).
For example when i start the first Everything.exe i might have disabled my (C:) drive from the Index but when i open the other Everything, let's call it - Profile 2, i can only search files from (C:).
This is for separation basically, if i don't wanna go into the settings and enable/disable the C drive all the time.
cloning Everything
Re: cloning Everything
Please see multiple instances.