@exarkuniv Ok now I feel extremely stupid for not thinking about this before. But because I'm probably not the only one, I figured I'd post this info in case others run into the same thing. After wasting more than half a day trying different HDMI configurations and editing the config file a million times, I realized that by plugging in HDMI 1 into the lcd controller and using HDMI 0 as the output source for a bigger TV, the pi will always check HDMI 0 first for signal and if it doesn't find one, then it goes to HDMI 1. So in other words, no need for an HDMI switch or splitter. Man I feel so stupid but at least the problem is solved now.

Please post some details about your setup, as requested in https://retropie.org.uk/forum/topic/3/read-this-first.

Post the verbose log when running an emulator to pastebin.com to take a look.