All crafting is done in the Crafting Window (Forge), which is opened with the F key by default. Crafting using Forge can be done anywhere at any time.
After placing an item in the slot at the top of the window, you can either add a Shard to the item by selecting one of the affix slots to fill and choosing an available affix or choose a Rune by clicking on the Rune icon. You can also choose to use a Glyph in the Support Item slot, if applicable.
If an item has any Forging Potential remaining, you can use Shards and Runes on it. When an item runs out of Forging Potential, you can't alter it further in the Forging Panel.