Problem when altering 2nd runes, since reforged

Sorry guys, this seem a minor one but it frustrated me since the beginning. I have not scroll through the posts to check if its already posted, sorry in advance.

When I why to alter one of the two runes of the 2nd tree, it usually end up a mess. Say, I have A and B for the 2nd tree, now I want to switch B out for C. It might come out as tree with C and B instead.

It been like that since the reforge came, so I guess you got my idea. So is there some better ways to change the runes or somethings?

Thx