There are many types of subordination and it is not possible to give a simple answer, a simple criterion. However, sometimes it is the very presence of a subordinator (or of a relative word) that makes a clause subordinate. Compare
 a. I saw him and I stopped my car.
b. W̲h̲e̲n̲ ̲I̲ ̲s̲a̲w̲ ̲h̲i̲m̲, I stopped my car.
c. I saw him w̲h̲e̲n̲ ̲I̲ ̲s̲t̲o̲p̲p̲e̲d̲ ̲m̲y̲ ̲c̲a̲r̲.
In [1a], there is no subordination at all; instead, we have a coordination of two independent clauses, the clause I saw him and the clause I stopped my car.
In [1b] and [c], we have subordination (the underlined clause is the subordinate one). But which clause is subordinate and which principal is determined by the placement of the relative word when (and of the comma).
So it's not necessarily the case that you first somehow decide which clause is subordinate, and then place the relative word accordingly. Sometimes it is the other way around: sometimes it is the placement of the relative word that determines which clause is subordinate.
And the placement itself is then ultimately determined by the meaning: in [1b] the seeing happened first, followed by the stopping of the car, whereas in [1c] it is the other way around.