Do all instances of OP share the same config files?

What is the problem?
I have a Windows 10 machine dedicated to controlling 2 Lulzbot Taz 6 printers. IT department won't let me use RaspberyPi so that is not an option. I have followed tutorials to get two instances of OP running, each controlling 1 printer and this works. However, it seems like the two instances share the same configuration file so I am having trouble with little things like default connections, appearance etc. Is there a way to have two totally different installs of OP that don't share anything?

What did you already try to solve it?
Installed, followed windows tutorials, searched google. Not easily finding info on how config files work etc.

Additional information about your setup (OctoPrint version, OctoPi version, printer, firmware, browser, operating system, ... as much data as possible)
Windows 10
OP - 1.3
Lulzbot Taz 6 printers

If you run them on the same machine under the same user, then yes, they will default to the same config location and hence share it.

Take a look at the --basedir command line option, that's probably what you are looking for. See also