Can you use them in there or can you only use red/green/blue ones acaording to the mutation set?

You can, but I'm not sure if it's supposed to work like that. Take a look at this: https://www.youtube.com/watch?v=p0eiPPwcyHY

Well I guess it isn't which continues to make those skills kind of bad.

I've only ever invested in Cat School Techniques and Strong Back. The first one I find particularly good if you plan on visiting the Rune-wright for the enchantment that treats all equipped armor as Light Armor (forgot the name) while using the Ursine Witcher Set with bonus to Adrenaline Point generation combined with the Whirl Combat Skill. The second I find most useful because I can actively swap Axii Lv.3 (which I use mostly for conversations) for it whenever I get over-encumbered. If I had to choose one, I'd go for Strong Back, since the game's not particularly difficult, even on Death March! with Enemy Upscaling enabled.