Trib, no secrets nor wizardy in ChkMods...
The way you describe to operate it is the correct one, if you still run into issues, just report them....
ChkMods works by taking a working installation of 1946, all patched up to whatever MOD version, and of that version, all the relevant files (just about everything, except missions, paintschemes, and the likes) are being recorded version wise, and that info is stored in a database.
When checking, it checks all those relevant files with your installation, anything missing will be added, everything of the wrong version will be replaced... that's basically all...
As it does not check all files, it is best to start with a complete installation of a version, though it is possible to start with an empty folder. You will then end up with a multiplayer-client version, as there are no missions, not even quick ones.
And, for sure, you will need to set up the hardware settings, in conf.ini, and your key- and controller assignments....
UP3 is history, History is current...
(The H in HSFX stands for 'History':) )