File > Export > Adobe PDF (print)
Export your body/inside file as Pages
Export your cover file as Spreads
Marks & Bleeds
Check Crop Marks, Bleed Marks, and Use Document Bleed Settings.
Check Video PDF after Exporting to be sure that your PDF file looks correct.
Make sure to open your PDF in Acrobat.
When you open your two files in Acrobat, this is what they should look like
If you want the inside of your cover to be something other than the paper color, make sure your cover file has two pages. The inside of the front cover is on the left and the inside of the back cover is on the right.