First, read up on Item Set Collections if you haven't already. If you have, you should already know a couple key facts:
- As you unlock more pieces of a set, the Transmute cost to Reconstruct the items from that set decreases.
- No matter how much the item cost to Reconstruct, you will always get 25 Transmute Crystals back when you Deconstruct it.
- The minimum Transmute cost for Reconstructing an item is 25 Transmute Crystals.
- Mythic items cannot be Deconstructed.
With this in mind, use the Transmute Station to Reconstruct items from an item set that you have completed - that is, a set that only costs 25 Transmute Crystals to Reconstruct. I use Arena bows - specifically the Blackrose Bow ("Virulent Shot") for this purpose, but any piece of your choice from any set that costs 25 Transmute Crystals to Reconstruct will do!
Reconstruct however many items it takes to store the number of Transmute Crystals you intend to store. For example, if you want to store 500 Transmute Crystals, Reconstruct 20 items. Not Mythic items! Remember, above, where I said they can't be Deconstructed!
Once Reconstructed, store the items wherever you choose. I prefer to use 60-slot Storage Chests, because you can achieve a storage density of 1,500 Transmute Crystals per 60 slot chest, and I don't need to swap characters to dig in to my stach of Transmute Crystals. Storage characters are also perfectly valid, as is your Bank.