Hi, from what I understood from the readme the major skills have more importance to attributes than misc skills. But I don't have any skill with willpower on major or minor, so if I train misc skills with willpower as governing attribute how effective will it be? My character is very weak against magic so I really need magic resist.

Without Willpower as a primary attribute for anything above a Misc. skill, it will be difficult to raise it significantly. Then again, if your character has high initial Willpower, you may still see a moderate degree of improvement by raising those Miscellaneous skills. In addition, there are several other skills (Mercantile, for example) which will give it a lesser boost as a secondary attribute. GCD is somewhat brutal in that respect, where if you don't have it to start, you can't really get good at it, but you can still improve it somewhat. It's one of the reasons why about half my characters use MADD Leveler instead, because I want to make a character with a few odd "twists" that GCD penalizes.

By way of testing, if you run GCD on a fresh character, open the console and type 'player->set(majorskill) 80'. Do the same for a minor skill and do it again for a misc. skill. You'll see the major skills will be set to 80, the minor skills to around 76, and misc. skills will end up at 72. That gives a rough idea of how the attributes will skew over time. I think it's a nice feature and is one reason I stick with GCD. Race and class do matter!
All attributes will advance. Under tough circumstances, though, you might find you'll simply have to compensate for a weaker one with a spell, potion, or trinket.