A simple thing, so a short post. To split a layer in After Effects, the hotkey shortcut is Cmd+Shift+D. This will split the layer at the position of the Current Time Indicator (the red line). You can also select the layer and choose Edit -> Split Layer. This will work on audio, video, or image layers.
There are probably many other ways, but this worked for me. Open your file, click ‘Save As’, then choose .gif as the filetype. Click on the ‘Options’ button
Then select ‘Index Transparency’ in the dropdown box on the lower left.
Save your file and done!
If anyone has a better method that deals with anti-aliasing better, please let me know!