If you've already completed level 1 and have built the AW, then additional Rune Shards will simply accumulate in your inventory. You'll need them to upgrade to level 6.
If you have Rune Shards of a type that you DON'T want, then you can convert half of them into something useful. 10 Rune Share of an unwanted type are worth 1 Rune Shard of a desired type.
While you're filling up an unwanted Rune Wheel, so level 1 for our purposes, you'll break half the Rune Shards of the relevant type. When your Broken Shard bar is full THEN you switch to a DESIRED AW and use the full Broken Shard bar to fill in an empty slot in the desired Rune Wheel.
You don't even need to build your unwanted AW. If the Rune Wheel is already full then half of the shards will break and go into the broken shard bar, and the half that WOULD have filled a Rune Wheel Slot are simply lost.