I made two 5V supplies in my schematic that I wanted to be independent from eachother, 5v for internal power and 5V for external power going off the board. I’m trying to understand why the 5V outputs are connected even though they have different names.
How do I made it so they aren’t connected? Do I need to add power flags for each of these 5V sources?
Check the power symbol you created. The resulting net name depends on the invisible pins name not on the value of the power symbol. (my guess is that the pin has the name +5VA)
Details about power symbol creation see this part of the make a symbol tutorial: Tutorial: How to make a symbol (KiCad v5.1.x)
If this is not the source of the problem then check if you have shorted the two nets somewhere. (You have connected both to +5VA somewhere)
You were correct! Different “names” but hidden still had the name +5VA. Darn @Rene_Poschl you are on your game 
Thanks for the help!
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