The purpose of the "splitgrade mode" is to tie the two channels together so that if you adjust one channel, the timer automatically adjusts the other channel to maintain the same contrast.
For example, you have determined that Channel 1 is 15 seconds at grade 0 (say 200 units yellow) and Channel 2 is 25 seconds at Grade 5 (say 200 units magenta) is the appropriate exposure for your print and you have a series of burns programmed into each channel. Then you decide that you want to print the whole thing 1/6 stop darker. In the split grade mode, you just nudge up one of the channels base exposure by 1/6 stop and the timer adjusts all the other times to maintain the same overall contrast for the print.
In the disconnected mode, the two channels are completely independent of one another so adjusting the exposure in the soft channel has no effect on the hard channel and vice versa. That is the mode I use. I might have the explanation a but wrong because I never use the split grade mode but I think I am on track.