Tip: Switch palace switches normally disappear if you replay the level. However, if you insert them as direct Map16 and use the hex-edit at $00EEB2 in the ROM map, you can replay the level without a problem.
Start by extracting all your GFX files from your ROM by pressing in Lunar Magic
Then in the editor you go to "File > Load GFX > Load GFX 0F", navigate to your ROM folder go to Graphics and then select GFX0F.bin
Do the same with GFX10.bin, after you did that the window should appear with the "Mario Start" screen.
"Patch ROM Directly" means that it inserts the changes directly into your ROM without generating a patch that you insert with asar first.
"Patch ROM Directly" does not support all features the patch generator does (Like the row patch)
Do you mean it won't show in-game or in-editor?
In case of it not showing in-game are you sure you selected the screens in the patch settings? Also, are you using SA-1 or not? Either way you can send me the patch it generated and I'll look at what's going on.
In case of it not showing in-editor you can try loading a screen from rom or from the template file.
If it doesn't work you can send me a patch of the rom it failed to load from so I can see what's going on there.
If you want to change it in-game then do that in lunar magic:
Open the palette editor, uncheck "Enable custom palette for this level" and edit the palette there.
Note that some colors might not be loaded meaning that they'll use the last loaded value for that color
I do not know if lunar magic changes that.
If you want to change the palette the tool uses then export your palette and open it via "File > Load Palette"