this has been pi$$ing me off for days. First time playing Icewind Dale 2 and after a few levels I have skills like Concentration: 12 (9). gone through the manual with a fine tooth comb and wasted hours trawling forums but cannot see what the effective level is. What is my skill level... 12 or 9 and why they display them both?

aaaaaargh :(

9 should be your effective skill.
I guess you used the stat that govern Concentration as a dump stat?

Putting some points in charisma for clerics may be useful to turn undead. Yes, there isn't as many undead as in IWD 1, but still may be worth it (unless you really prefer "manual solution" with mace).

It should be in the manual.

The value in the parenthesis is the base value, the other value is the value adjusted for buffs/debuffs/stat modifiers etc. Your current effective Concentration lvl is therefore 12. Note that for the purposes of perk requirements you need to reach that requirement with your base value.

Concentration is constitution based. You can check in your character record -> information -> skills.

An exception are the perks which grant 5 elemental resistance and 20 percent extra elemental damage like scion of storms. For those the int-modified skill value is checked.