A better way to do this would be to render the tracks to audio. That would get rid of the first issue.
For the second issue, I'd consider utilizing the Live Loops mode. You can drag the rendered audio into there and trigger them as needed. When set up correctly, you can move from major to minor on a beat and prevent pops.
Also, it may be unrelated now but when setting up Logic for performances, meta events can be very helpful https://support.apple.com/guide/logicpro/meta-events-lgcp2158b34e/mac