You can use the simulators to test and run things, but indeed, unless you change your geographical location to shift night time, twilight will remain twilight
Here's my take at your original M101/NGC6888, done from Rennes, France.
I add a new job, M101, with default restrictions (asap, alt>0, twilight). Scheduler says job starts at 11:06pm today.
I add a new job, NGC6888, with default restrictions except for Alt, where I set 38 degrees. Scheduler says job starts at 03:18am tomorrow.
I use a dummy 11x1s sequence for those two jobs, so Scheduler says job 1 ends at 11:09pm, and warns job 2 has more than 4 hours of lead time. I'm only interested in start times for now.
Now I know that I have roughly 4 hours available for the first job, so I configure the first job to run until tomorrow 3:00am(completion condition "repeat until"). Lead time to next job is now 18min.
Then I configure the second job to run until terminated, knowing that the twilight restriction will abort it. I make sure the preemptive shutdown is configured with 1 hour.
From there, I can change the sequence files to whatever series of captures I need. If you need multiple filters on the same target, you may duplicate the scheduler job, change the sequence file and adjust the completion condition to keep NGC6888 starting at 3:18am.
You probably noticed it, but the UI flow requires you to double-click on existing jobs to edit them. In order to duplicate a job, you edit it, validate the changes with the checkbox button and immediately click the + button to add another instance of it. This is admittedly not very user friendly, and should improve soon.
-Eric