Fortunately, Matlab Apps are available as source code.
So, let us see: In line 158,159 of PAMGuide.m we find
xbit = xbit(:,1); %In case of multichannel input, selects
%1st channel (use xDIG(:,2) for 2nd, etc.)
which answer your question: it is 1st channel.
To select other channels you have to xbit(:,1) to xbit(:,2) for second channel etc. (Note: I consider xDIG to be a typz or left over of an earlier version and should read xbit, otherwise it would not make sense)
There is no menu-entry for selecting the channel, but it is easy to modify the source code. And if it is really important you can add a small text-box onto the menu and change channel from GUI.
EDIT: the real location to edit is PG_Func line 235! It seems that the statement in PAMGuide.m is of no impact as xbit will be cleared a little bit later.
Comment: PAMGuide is nearly 10 years old without any visible maintenance on Sourceforge. Maybe time to replace it?