When you say you have 'skarner', what do you mean? Champion permanents are a thing in hextech crafting that results when you reroll 3 champion shards, and allow you to permanently unlock that champion (as if you'd bought them in the store). Champion shards are another thing in hextech crafting that allow you to temporarily 'rent' the champion if you don't own it for a week, so you can try out the champ.
Simply owning the champion (e.g by buying it in the store) is not the same as having the champion permanent. That said, in the majority of cases I don't think one would want to unlock mastery 6 via a champion permanent. If you happen to get lucky and get a champion shard for the champ you want to unlock mastery 6/7 for, then hold on to it and use the champion shard option. If you don't, it's much more reliable to simply disenchant ~3 champion shards into blue essence and use that option to unlock the next mastery level, rather than rerolling the 3 shards and hoping to get a champ permanent for the champion you want.
Also, do you have 2 level 6 mastery tokens for skarner in particular? You can't use mastery 6 tokens earned for other champions to unlock a different champions mastery level.