It's a bit complicated, but I'll try to explain...
As for the term itself:
Schutzhaftlagerführer could be translated as "Protective Custody Camp Leader"; Lagerführer is just a shorter, somewhat "colloquial" version of this designation; it does not describe a different duty position and does not refer to the camp commandant.
As for the Schutzhaftlagerführer's place in the camp's hierarchy:
A concentration camp's administration broke down into five Abteilungen [Departments]:
Abteilung I - Kommandantur-Stab [Commandant's Office Staff]
Abteilung II - Politische Abteilung [Political Department]
Abteilung III - Schutzhaftlager [Protectice Custody Camp] also known as Häftlingslager [Inmate Camp]
Abteilung IV - Standortverwaltung [General Premises Administration]
Abteilung V - Sanitätswesen [Medical Matters]
The Schutzhaftlagerführer was the head of Abteilung III (Schutzhaftlager/Häftlingslager) and as such, wielded considerable power as he was in charge of running the actual inmate camp and thus of controlling the inmates (of all inmate categories, naturally), which also included the responsibility for maintaining "order, discipline and cleanliness" and for punishments.
His immediate superior was the Lagerkommandant [= Camp Commandant] as whose deputy he also functioned.
(Larger camps could have up to four Schutzhaftlagerführer, who where in charge of different sections of the camp. In this case, the senior one - who functioned as the Deputy Commandant - was called Erster Schutzhaftlagerführer [= First Protective Custody Camp Leader].)
Subordinate to the Schutzhaftlagerführer were the Rapportführer [= Reporting Leaders], Arbeitsdienstführer [= Labor Duty Leaders], Blockführer [= Block Leaders] and Kommandoführer [= Work Detail Leaders].