I'm planning to use a ATmega-M1 for a switching power supply. The built-in power stage controller PSC is a nice fit. But some of the PSC output pins cohabitate with ISP functions. For example PSCOUT0B is on the same PIN as SCK. As PSCOUT0B is wired to my switching hardware this looks like a bad idea.
Now there seem to be a full set of alternate pins for ISP. There is SCK_A, MOSI_A, etc. The seem to be better placed (not on the same pin as a power-output). But I'm missing a clear understanding how I can choose between the two sets of SPI pins. From the Serial Programming part of the data sheet I have even the impression that the _A pins are to be used for ISP.
A bit confused and looking for clarification