It uses Microsofts standard settings saving feature, which unfortunately saves things to an obscure location hidden in AppData.
I've tossed around the idea of having settings and inventories synced to the EQResource server, which would allow syncing across computers and allow inventory to be viewable on site (admire your loots while at work! lol!). I'm not sold on this feature idea, as it's a good bit more stress on our server, which is already close to needing an upgrade again! This may get put in as a Premium Member only feature to keep the load down. I'm not sure yet, so don't take this as a "this will happen" statement :p
Was there some bug or issue with the software that caused your characters to be unlinked?
As far as uninstalling, you can find the program listed as "Multi Character Inventory Manager" in your add/remove programs section in control panel. Click start, begin typing "remove a program" and it should pop up quickly under "Best Match". From there, browse the list of installed programs on your machine and find "Multi Character Inventory Manager". Click on it, then click uninstall and follow the prompts.