I want to know if a program can run two threads at the same time (that is basically what it is used for correct?). But if I were to do a system call in one function where it
Yes, they would, at least potentially, run "at the same time", that's exactly what threads are for; of course there are many details, for example:
If both threads run system calls that e.g. write to the same file descriptor they might temporarily block each other.
If thread synchronisation primitives like mutexes are used then the parallel execution will be blocked.
You need a processor with at least two cores in order to have two threads truly run at the same time.
It's a very large and very complex subject.