Can't get screenplay to compile

I made an outline on index cards. I split the screen and started writing sections of the script in Scriptmode. After I had some scenes done (each connected to an index card) I tried to compile my work. All I can compile is a longer text document having all the info from the index cards. I don’t see how to compile the screenplay created in the split off window.

Depending on how I read that, that sounds like what Compile is supposed to do. It takes the contents of all the cards, the stuff you typed into the text editor in script mode, and glues all of that together into a single file. But maybe I don’t understand what you mean by “the info from the index cards”. Do you mean the text that is gathered into the compiled document is the Title and Synopsis from each card, not the script? If so, maybe you chose a compile preset that is designed to do just that, such as the “Synopsis and Titles” preset that works just like you’d expect. I’m not sure what type of script file you need, but try selecting “Script or Screenplay” from the Format As compile drop-down. That should at least get you back into the realm of normal, from there you can change what settings you need (maybe you need something other than Final Draft FDX format).