Hey man, you can definitely do what you're trying to do. I just sold my Minilogue last week, but I sequenced it with my BeatStep Pro and my KeyStep.
I ran mine with the ML set to slave.
It's okay to let the ML sequencer run, you just need to delete the sequence. I think the command was shift + rest. If you want the ML sequence back just change to a new program and then change back again. If you delete the ML sequence and save the patch then the sequence will be gone for good, if you want to keep the patch as is you can just delete the sequence and save the patch to an empty slot.
As for the other issue, sorry but I don't quite understand what you're saying. Do you mean that pressing the numeric buttons (1-16) is not triggering notes on the ML? If this is the case be sure that the ML is set to receive clock, that one of the 2 melodic sequencers are active, and that the ML is set to receive MIDI on one of those channels. (By default BSP transmits the melodic sequencers on channels 1 & 2 respectively, and the drum sequencer on channel 10.)
Make sure your cables are connected correctly (sorry, super obvious but it doesn't hurt to mention it). If running the BSP & ML standalone (no daw) with BSP as master then be sure the BSP sync setting is set to INT (internal clock).
Hope this is helpful.