The best form of remembrance is the Quran and the best way to read the Quran is in your nawafil, Qiyamu-layl or supererogatory prayers.  

This is the khairu Dhikri.  As you recite your Quran daily, you are doing your dhikr.

Please note that in your two unit rakah of Qiyamu-layl, you will combine most of the azkar. You have the opportunity to combine the takbeer with tasbeeh, the istigfar with salawat and then with the Holy Quran.  You have all these in your Qiyamu-layl. You can see it is amazing!

The most important part of your salat therefore is your recitation and your sujud. The flexibility is that you are allowed to do your recitation as long as you can possible go, and reflecting on the meaning. The second part is sujud where we do not recite Quran, but tesbeeh and dua. 

Umu Salama narrated two hadith on the prophet prayers; she said the Prophet would spend the entire night with one ayah of the Quran. At another time, it would be as if he would recite the whole Quran in his Qiyam. When he stands, reading the quran, he would bring up dua to Allah SWT.

And when he makes sujud, he would spend longer time in sujud, so long that you will think he had passed on in sujud.

The bottom line here is that he engaged himself in zhikr and dua. So engage yourself in the Quran recitation and dua, which you say to Allah in sujud. There is flexibility here, you can do either of the two in your Qiyam layl.