what you initally asked, about how to change the bassline's pitch every 2 bars can be done by simple automation:
first copy/paste the pattern from a1 to a2, then in a2, make the pitch changes you want, then do the same to a3,, a4,, etc...
now, there are two ways to change the patterns:
1. right click on the matrix pattern numbers, and click 'edit automation', then on the sequencer, draw the desired pattern number for each section.
2. click on the matrix sequencer track so that the input icon will appear next to it, click record, click play when ready,, and change the pattern real time,, when you finish, press stop and the automation will be there.
ofcourse you can also do what hey cheggy suggested and draw the patterns directly on the main sequencer instead of the matrix (i prefer the matrix for simple melodies/basslines).
all in all, enjoy! 
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