Basically there are 2 options that were added to handle level bonuses so the GM can use any of the options in Character Law plus the groupings from RM Companion 2. You can find them in the Options, Optional Rules (GM) section.
The first option is ChL #23: Level Bonus Grouping. It allows you to select None, Core, RM2 (Opt23.1), RMFRP (Opt23.2), or RM Companion II.
* None - The players and GM have to manually set the level bonuses. This is only needed if one of the other options doesn't work.
* Core - Uses the groupings from Character Law section 9.3. There are only 2: Combat and Spell.
* RM2 (Opt23.1) - Uses the groupings from Character Law Optional rule 23.1.
* RMFRP (Opt23.2) - Uses the groupings from Character Law Optional rule 23.2.
* RM Companion II - Uses the groupings from Rolemaster Companion 2.
The second option is ChL #23: Level Bonus Type. It allows you to select Core, Stepped (Opt23.3), or Static (Opt23.4).
* Core - Uses the normal +1 to +3 per level from Character Law section 9.3.
* Stepped (Opt23.3) - Uses a staggered approach to applying level bonuses as explained in Character Law Optional rule 23.3.
* Static (Opt23.4) - Uses static level bonuses as explained in Character Law Optional rule 23.3.
After those are set to what the GM wants to use in their campaign, it should automatically calculate the level bonuses appropriately for the skills in Character Law and RM Companion 1 (if it was bought from the FG store). If the GM wants to use skills from another companion, they just need to select which (if any group) the skill is a part of based on the option selected in ChL #23: Level Bonus Grouping. This will tell the ruleset which level bonus to use from the profession based on the skill grouping and optional rules selected. The GM can also change any skills they want to different groups by modifying the skills.
The professions have the actual level bonuses. There is a separate tab L. Bonus That has each of the groupings with the groups for each grouping. That is where the level bonus is entered for the group. The ruleset will use what is selected in option ChL #23: Level Bonus Grouping to figure out which value to check for on the profession. Then it will figure out how and when to apply the level bonuses based on ChL #23: Level Bonus Type.
After updating a skill or profession, the GM will need to right click on it and choose Share Sheet from the radial menu so that it gets pushed to the players copies.
It isn't completely customizable but it is very flexible. Please let me know if that doesn't clear things up.