1. Glimmer is main currency for buying upgrades, gear, vanity stuff etc.
2. Materials like Spinmetal (there is others too) are raw material that can be used for upgrades, sold for cash or reputation. I would hold on to them and use them for gear upgrades when needed.
3. Token [Vanguard or Crucible] are gained by doing quests for them, PvP etc. You can gain 100 / week. Used to buy gear.
4. Motes of Light are "end-game currency" that are gained through gaining XP at level 20. Used to buy gear.
5. There is also items called "Strange Coin" that you should hold on to
Thanks. Isn't rep more important than upgrades, though? Is there a reason to upgrade weapons if they're not legendary or the top rank?