This is not supported by AMT 1.1, but there is an unsupported workaround found on a MultiMedia bulletin board (posted by Don Leatham):
Tools needed: ResEdit 2.1.1, AMT 1.1, DeBabelizer
Step 1 - Use the Runtime Maker to create your Mac application.
Step 2 - Use DeBabelizer to create and save a Super Palette for your artwork. When you make the SuperPalette in Debabelizer, make it for 254 colors instead of the normal 256. When you paste your Debabelizer 'CLUT' resource into your program's 'pltt' resource you won't loose any colors.
Step 3 - Start ResEdit.
Step 4 - Using ResEdit, open both your Mac application (from step 1) and your "DeBabelizer Prefs" file (inside your System:Preferences folder) You will see in the prefs file a resource type "CLUT"
Step 5 - Open the "CLUT" icon in the prefs file.
Step 6 - Open the Supper Palette that you created (in step 2)
Step 7 - From the Edit menu do a "Select All" and a "Copy"
Step 8 - Open the "pltt" resource in your Mac application
Step 9 - From the Edit menu do a "Paste" command. Click "OK" to the warning.
Step 10 - Close and save your Mac application.
WARNING: The "pltt" resource maintains its first two entries as black and white. When your Super Palette (which is actually a "CLUT" and doesn't have this restriction) is pasted in to the "pltt" you can get some pixels switched in some images this may be a problem.
ANOTHER WARNING: The Runtime Maker has a bug in that it creates applications that do not reset the palette back to the System Palette when they quit. Therefore, if you use this workaround, your super palette will be applied to the Finder after you quit. This could possibly cause some end-user support problems.