Salam. When I talk about all the times I’ve missed my prayers, my teachers at school and friends tell me that next time I pray, I pray that prayer twice, in order to make up for all the prayers I’ve lost. I’m just making sure this is true because I’ve already started doing it. Another question is if it’s true,, which prayer comes first? The actual fajr prayer or the makeup fajr prayer? And how do you distinguish the two prayers? Please let me know anything I should know about making up prayers. Because I’m trying my best to get back on track. Thank you
In the Name of Allah, the Most Gracious, the Most Merciful.
As-salāmu ‘alaykum wa-rahmatullāhi wa-barakātuh.
Alhamdulillah, it is a sign of your Imaan that you have a concern to make up your missed prayers.
In principle, it is necessary to make up all missed prayers from the time one reached puberty. If one is not sure of the actual number, then he/she must apply the mind for an accurate estimation.
An easy method to fulfill this obligation would be to repeat one missed prayer along with every Fardh and Wājib Salāh you perform. For example, after you finish Dhuhr Salah, then one missed Dhuhr should be performed. Hence if three years of Salāh were missed then after three years all the missed prayers would be made up.
The Qadha Salah may be performed before or after the actual Salah of the day. Both ways are permissible. The factor that distinguishes between the missed prayer and the actual prayer is your intention.
As a general principle, it is preferred to make up missed prayers instead of engaging oneself in optional prayers. However, those prayers that have been specifically mentioned in Ahādīth (such as the emphasized Sunnahs and the optional prayers such as Salah adh-Dhuha and Tahajjud) should not be missed even if one has to make up missed prayers.  If the above-mentioned method of making up missed prayers is adopted, then one will easily be able to perform missed prayers as well as these virtuous optional prayers.
Note 1: There is no Qadha (making up) for missed Sunnah prayers. Making up is only in missed Fardh and Witr prayers.
Note 2: While performing the missed prayers, for each prayer make intention that this is the first prayer I have missed in my life after reaching puberty. For example, when making up Dhuhr, make intention this is the first Dhuhr I have missed in my life. Thereafter, make the same intention while making up the next Dhur, as the next Dhuhr missed will now be the first Dhuhr since the previous one is already made up. 
And Allah Ta’āla Knows Best
(Mufti) Abdul Azeem bin Abdur Rahman
The Shar’a ruling herein given is based specifically on the question posed and should be read in conjunction with the question.
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 وأما النفل فقال في المضمرات: الاشتغال بقضاء الفوائت أولى وأهم من النوافل إلا سنن المفروضة وصلاة الضحى وصلاة التسبيح والصلاة التي رويت فيها الأخبار. اهـ. ط أي كتحية المسجد، والأربع قبل العصر والست بعد المغرب (رد المحتار، ج 2، ص 74، سعيد)
 Aap Ke Masaail Aur Un Ka Hal, Vol. 2, page 351