i read over the pattern sequencer sections of the owners manual again and i saw another thread about this but the problem was never really solved in it so I am reposting.
can patterns not be recorded in keyboard mode? whenever i sample something and select it with the sample selector, i am unable to record clips in the pattern sequencer of me playing that sample in keyboard mode. the recorded pattern will instead play the samples it would trigger in sample mode if i had pressed the same keys. even though the pattern sequencer seems to have a keyboard mode sample select parameter, selecting the sample i am using does not seem to do anything.
recording patterns in keyboard mode
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You need to know that keyboard mode can only use one sound from sample mode at a time, so you assign a sample to keyboard mode, record a pattern, select another sample for keyboard mode, record next pattern, and so on. It's a bit fiddly but it is possible to create complex pattern based music pieces using the MS. 

microSampler Rocks!