I looked at the TU0_Disable() method of the TU0 PEx component....it disables the *entire* peripheral. How do I disable the output of just a selected channel? The Vybrid RM mentions an Output Mask (section 39.4.15). This would be ideal, but PEx does not provide an interface for it.
Perhaps I just need to use the FTM_PDD_WriteOutputMaskReg() macro in FTM_PDD.h? However, there is no Read version of this macro, so in order to not clobber the existing bits, I'll have to call FTM_OUTMASK_REG() instead: Once for read, then OR my bits, the write it back. Is that going to work?
On Edit: I verified that this indeed works. Using the FTM_OUTMASK_REG() macro is all you need to manipulate the Output Mask of each individual channel.