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So first of all, the city where i live there is only a small shop which sells warhammer 40k products, so we are kind of unofficial GW store, and we had only recently start playing warhammer, like 1 year ago.
so only this few months we have really trying to make tournaments as official as possible with what we got.

My question is the next (keeping in mind we got about 8-10 players willing to play the tournament) my friend is trying to organize a tournament in pairs or by teams if you prefer, and i was wandering how important is that the team belong to the allies matrix, i mean is it really a tournament rule that i cannot play with my friend that has CSM while i am a Space wolves player?, this 2 faction rule is really getting to us because we don't have enough players of both sides to make the teams. i now the fluff comes into play here but we are trying to start something

i wanna hear your opinions

The Allies matrix is only when you want to play One *army* from 2 codexes.

2 vs 2 games you are free to use whatever you like

i was asking more about the othere ally matrix back in 5th edition i think there where 2 sides

Good guys Bad guys
All marine codex Chaos space marines
Imperial guard Chaos demons
Tau Necrons
Eldar Dark eldar
Tyrnid

You don't NEED to follow whatever GW implements for tournaments, specially since there has not been anything official from 6th however i guess this is what you are looking for:

http://www.games-workshop.com/MEDIA_CustomProductCatalog/m1470393a_WHW_40K_doubles_event_pack_2011_PDF