If you are, your experience is going to them instead. When you wear a faction item (Dead Orbit, New Monarchy, Future War Cult), both vanguard and crucible bounties all go to them. Doing this in the beginning is probably the best if you play both PvE and PvP because it's all pooling into one thing.

If you are wearing a non-faction class item, Vanguard bounties will be applied to the Vanguard. Crucible matches and bounties will be applied to Crucible.

Remember that marks are capped at 200, so spend them. Otherwise you've not been getting new marks to spend.

You get ascendant materials (shards and energy) from doing public events, and the most consistent way way (aside from raiding) is to do the daily heroics every day, although I think it's the level 27 and 28 heroics and not the 26 that gives out ascendant materials. You can also get ascendant shards and energy by dismantling legendary armor and weapons, respectively.