You can do whatever you want. It’s up to you to try things out and see what works best for you.
If you have a specific arrangement in mind where you want to the Digitakt and Digitone to work together, you can set up the Digitakt to control which pattern the Digitone plays. But if you want more flexibility, it’s perfectly OK to change the pattern on the Digitone manually.
Similarly with sequencing, if you want Digitakt to do all the sequencing then it can. However, you may find more flexibility if you program the Digitone’s patterns in its own sequencer and then synchronize the two sequencers using MIDI.