the items you collect from amomalies are part of the crafting system (done mainly on Memory Alpha), which can be used to upgrade your existing equipment (ex. upgrade a MkII Personal Shield to MkIV using the original equipment, and the various crafting ingredients needed)
and the more things you upgrade, the higher tiers you can upgrade to (it is a skill system after all)
oddly, you can't just make items out of these materials, you can only upgrade existing ones
I dont actually do much crafting, but you would go to memory alpha. Normally after your first few levels you pick up a quest that takes you there. But I am no expert, but i found this for you as i think it wil be more help than i can be. Hope this helps:
In that guide, they say MK IV only, butt of course you can also craft MK VI items there, such as MK VIII and MK X in the Tier 3 areas. I hope after Season 3 we will see Tier 4 vendors selling MK XII items.