In order to install TWiLight Menu, you indeed have to replace the TTMenu.dat that comes in it.
But also, make sure you have your original Kernel in your SD, except for the TTMenu.dat of course.
If all you want is to try GBARunner, make sure you download the files from GitHub.
And also download YSMenu for TTDS, install it, and run YSMenu before you run GBARunner.
GBARunner2 ARM9 should be better than ARM7. I've found that ARM7 has audio delay that catches with the game every 3 minutes or so. I haven't found this Audio delay with ARM9, which is why I'm suggesting you to use it instead.