After much trial and error I figured it out. Here's how I did it in case someone else finds it helpful.
DetectHiddenWindows, On
DetectHiddenText, On
Run, Dolphin.exe "%1%" "%2%", , Hide
Sleep 3000
WinShow, Dolphin
WinActivate, Dolphin
$Esc::
{
WinActivate, LaunchBox Big Box
Sleep, 100
Process, Close, Dolphin.exe
ExitApp
}
Saved as dolphinlauncher.ahk and made in to dolphinlauncher.exe, with autohotkey, put in same directory as Dolphin.exe. In Launchbox make dolphin point to dolphinlauncher.exe, launch options "-b --exec=" with "no space before rom" checked. Nothing in the ahk section of launchbox. Works great, should be able to adapt it to other emulators pretty easily. Might need to adjust the sleep depending on how fast or slow your computer it.