The first book has a black werewolf-like creature on the front cover and I believe the third book was about a boy who could see coloured shapes and manipulate them into creating portals to other worlds/dimensions.
The last time I read them was when I was in school.
The Demonata by Darren Shan? Started in 2005, ten books total.
The cover of the first book (Lord Loss, 2005) has a werewolf:
TVTropes has a character matching your recollection of a guy making portals out of coloured shapes only he can see:
Blessed with Suck: Kernel has always been able to see patches of light floating around, and can use them to create inter-dimensional demon portals. On one hand, it gave him his little brother, Art.. On the other hand...having anything to do with demons in this world will not end well for you. Particularly considering Art is Lord Loss's demonic maggot-infested pet baby. Plus, there's the whole "everyone thinks I'm insane" thing that he had to deal with.
Found with the Google query scifi book create "portals * shapes" which returned the series' Wikipedia page, which has the above cover as an illustration; the werewolf seemed promising, given the details you had provided.
