The idea, of course, is that you don't normally alter the molecular formula itself - the additions go into the adduct description. So ideally you want an adduct that explains any extra mass in addition to declaring the charge.
In your case, then, an adduct "[M+CH]++" is the right description, I think. But as you've doubtless noticed the current Skyline release isn't going to understand that properly, and will get the additional mass right but will complain that the single H implies z=1 rather than z=2. So for the moment yes, you'd have to alter the formula and use "[M+2]", which is obviously not ideal.
The upcoming Skyline-Daily release does a better job of this - here's the description from the code change for that:
- Honor explicit adduct charge declarations (e.g. the trailing "+" in "[M+2CH3+Cl]+") (#2929)
Skyline may occasionally improperly calculate the ion charge of complicated adduct descriptions (e.g. "[M+2CH3+Cl]" where we did not pick up on the contributed charge +2 of 2CH3, and only used the -1 of Cl). Adding an explicit charge declaration (e.g. "[M+2CH3+Cl]+") would formerly just cause an error, with Skyline insisting on its own (mis)calculated charge. Now Skyline respects the declared charge.
Skyline will still complain about obviously wrong declarations like "[M+2H]-".
Also, "CH3" is now understood as imparting a charge of +1, so "[M+2CH3+Cl]" is now handled properly.