Robert
1. Yes, the mega patch consolidated all of the mini-patches to bring any early version of Il-2 to 4.12.2m standard. It allows you to do a one time upgrade which in turns reduces the risk of corrupt upgrades.
2. Highly recommend you DO NOT put C.U.P. into the same game folder as HSFX. Very high risk for corruption.
Recommend having multiple copies of Il-2 on your PC. On my computer I have 5 x Il-2 games and these are:
Il-2 1946 ver. 4.12.2 Clean
Il-2 C.U.P. for ver. 4.12.2
Il-2 HSFX 7.03 for ver. 4.12.2
Il-2 1946 VPMod for ver. 4.12.2
Il-2 1946 ver 4.13
I named them as such so I am able to easily see what game version is being used.
To have multiple copies of the game, simply install Il-2 and patch it to version 4.12.2. This copy of the game is used as the base for all the other games (and when I screw things up enough I need to start over) so I titled it "clean." There are no mods, buttons, anything in this, only the base game.
Next I created folders and titled them according to the game version I will be using. Once the folder(s) are created, go back to your "clean" Il-2 game folder, and select all of the contents inside the "clean" folder. Select Copy then move to and select one of your new Il-2 folders and past the entire game into that folder. Repeat for each version of the game you plan to have.
Each folder now has the exact same game inside though the game folders are named differently. Then add your respective MODACT, MODs, etc to each of your game folders to bring that particular game version to the desire MOD. Now you will have multiple Il-2 games available for your gaming pleasure.
This method does take up hard drive space but reduces the risk of interference among different MODs.
Was this the "show me how to do it" you were seeking?