I want to make sure we're talking TextSoap 9, as the behavior has changed over the releases. The info here is based on TextSoap 9.
Is the issue specifically with moving them in and out of conditional actions (If Matches ..., Process List, etc)?
In my experience, moving an action out of the conditional can sometimes get tricky -- especially if you're trying to put an action that was inside a conditional right after it.
If you're putting items into a conditional, you can drop them onto the conditional action and they will be placed at the end of the contained list of actions.
You can click on the left arrow to collapse the action contents, giving you more workspace.
You can also you cut/paste to move items around. Select your actions, cut them. Then select the action you wish to have the inserted after, then paste.
One additional trick for really large cleaners is to use a Group action. A Group action is just a container. You can then collapse the action's children to hide them all.
And I'm open to any ideas you might have that you think would make it easier for you to manage actions in the large cleaner.