@bucktaylor100 said in Help with configuration:

What's the best way to configure the controls for arcade games

Arcade games can have different button layouts, so the emulator tries its best to map a regular RetroPad to the emulated system. Usually the D-Pad is mapped to the joystick, Start is mapped to P1 Start, Select is Coin, A/B/X/Y/L/R are mapped to the panel buttons.
You can customize these per-core or per-game through the RetroArch configuration menus - https://retropie.org.uk/docs/RetroArch-Configuration/.

What's the best mame type emulator

Start here.

Is there a way to have a favorites section or a simple way to get to a specific game without scrolling for 10 minutes.

Yes, you can press Y to toggle the Favorite flag in a game and you can enable the Favorite global collection, which will show as a separate system in the Emulationstation list of system.

How do you shut this down easily? Can I configure a button to do a shut down?

Yes, you can configure a button.

How do I configure the audio? Amp is on and plugged into pi. Amp has volume turned way up and I plugged a phone into the amp and it played so I know it's all wired correctly.

Use the Audio menu in RetroPie and choose the analog jack output as default.

If this was a windows based system I could have this all configured in a few minutes but unfortunately it's just not that easy with Linux.

Sure, just install Windows on the Raspberry PI and you're good to go :).