I know it helps to wake up in the middle of the night to remember dreams. But which is the best way to do so? Auto suggestion or using a clock 
Auto Suggestion is much less reliable than a clock, but clocks wake you up much more rudely, lol.
I’d recommend waking up at key points in the night, namely those times which are speculated to be straight after REM sleep, set your alarm for 4.5 hours which should be after one of these periods…it will make it much easier to remember dreams straight after one, and you will be less groggy
Use autosuggestion not for waking up but for remembering dreams on waking up, so think “When I wake up I will remember my dreams”
So the clock set to go off soon after a dream, coupled with this auto suggestion is going to be pretty powerful for dream recall 
Use your cellphone and put the alarmtone on a song with rytm and let the volume increase gradient.
It’s best if you’re well rested and caught up on sleep. When you are it should be very easy to awaken in the middle of the night briefly and should even come naturally.