There's no benefit in specific runes placement like you describe.
There's only 2 dimensions you can build your runes for hero:
- Type of rune for set bonuses (it's either 2+2+2 sets like Tree/Rock/Mist or 4+2 sets like River+Tree);
- Stats the current rune provide.
Still it's the most hard and unreliable part of the game even now because finding perfect rune for any hero is lottery.
As to second question - you can remove runes from any hero for further using the same way you do with lesser runes. It will just cost you bit more - 750 runicite.
You can do it manualy before inserting new rune or if you are want to insert rune where 5 star rune is, the game will ask you if you want to remove or to destroy old rune.