New to multiboxing, having issues

[Wubsie]

First issue is that the window I want to be WoW1(my main) always get moved to WoW2(where I want my alt) and vice versa, how do I stop that from happening?

I never really had an issue with the ready made scripts renaming my game windows incorrectly. Are you launching them manually or having the script do it for you? I would recommend the latter option. I will also point out that the scripts on the site are about a decade old and, for example, do nothing to deal with the hidden duplicate WoW windows issue.

Second issue I run into is that when I go to herb a node, one character will always go and land on the ground to herb but the other always stays slightly off the ground causing it to not herb the node, how do I fix that?

Well, the answer is as simple as you might expect. You need to land the character. You can bind a key in WoW to Sit/ Move Down in the movement keys section. Then make a movement hotkey for it so you can send it to your characters to make sure they are on the ground. That, or drop form before interacting with the node I guess.