Eh, it's the window itself - that's the problem. Everything's crammed into one window, and you can't change/move things around, or remove and add other stuff; It's just not customizable at all.
Here's a few things that should be in a separate window:
- Combo List. One per window is enough; let the user decide how many lists he or she wants to have at a time. Also, take the search and other abilities from the Combo Editor, and include them into that window.
- Tabbed lists. Organization is key - Resources aren't really marked properly as of right now. With this master list, different resources such as items, weapons, tile pages, combos, and sound effects are separated to different directories and files.
- DMap List. Not do you just have the Dmap name and type in an easy and accessible list form, you also have each screen listed, and their warps marked to where they go, and the items that are there. An advanced view could also keep track of combo IDs and various flags.
- Item Tracker. Heart Container Pieces, rupees, and quest-specific items are tallied here, along with location and conditions.
- Minimap, nothing else to say about that.
That's all I can say.
EDIT: Thought of something else - a Comment section. Screens and Dmaps are what it's for, to make notes about the screen. For example, an unset warp because the destination screen wasn't made yet. Also, include a notepad, letting people write down things that are specific to that quest.