Use the latest NeoGamma:
http://gbatemp.net/t219243-neogamma-r9-beta-test
and read the mini FAQ there.
I guess your 1st disc is on a multi game disc and the 2nd is a seperate disc? If yes:
It won't work in WiiGator's loader, in NeoGamma it should work as expected. If not select the GCM whatever thingy as 2nd disc and try it again. That might actually work in WiiGator's loader too.
If both discs are on seperate multi game discs:
Insert the 2nd disc in NeoGamma, press Z on the 2nd disc. Eject the disc, insert disc with 1st disc, and then play it. At the end of disc 1, switch the discs as expected.
If both discs are on the same multi game disc:
Just boot the game, at the end of disc 1, eject and reinsert the disc.
If both discs are seperate 1:1 discs:
It should work as expected in NeoGamma. If it doesn't that's either a bug in NeoGamma(and WiiGator's loader!) or there's something wrong with your burn.