YSMenu is your answer.
http://www.gbatemp.net/index.php?showtopic=97615
I dual-boot it with the regular R4 firmware and all is good. If a game doesn't work with the regular 1.18 R4 loader, the backup YSmenu firmware is there to cover you.
There are some tricks to make it dual-boot, but it's not that difficult to figure out how to do it and have ALL the functionality you have always had using both firmwares at the same time.
Unfortunately, I'm too drunk to give all the details at his time though. But I'll attempt to give an explanation as best I can at the moment...let's see how well I do at this...
First, you have your 1.18 firmware. Rename the _DS_MSHL.DAT to Moonshell.nds, but otherwise leave all the other files alone. Put it on your microSD.
Create the YSmenu using the link provided above.
After creating the complete YSmenu loader deal, decrypt the the _DS_MENU.DAT that the YSmenu program creates using R4crypt and rename it to _DS_MSHL.DAT
Throw all those files into the microSD. Everything should be good to go at this point.
When you first boot the R4, it will show the standard R4 menu, the middle icon (which used to boot Moonshell) will now serve as the YSmenu secondary firmware boot. You can boot games that don't work with the normal 1.18 R4 loader through YSmenu's loader instead.
To boot Moonshell, use the YSmenu loader (accessed through the R4's old Moonshell icon) and locate the Moonshell.nds file to get to Moonshell. You should be able to reset from Moonshell to the main screen by hitting the start button and it will take you back to the R4's loader menu.
I have found this to be a way to have ALL the functionality of the original R4 loader, plus dual-boot with the YSmenu and still maintain compatibility with the games you want to play. Generally speaking, if a game doesn't work in the one of the loaders, it will work with the other.
I hope that makes sense to you and I hope you can work it all out and get it going. No one should be without their free games.