The rims of both balljoints have two notches in them, 180° apart. If you look closely at the control arms, they have a little divot or chisel mark, or a nub on the outside that the notch should line up over. If your manufacturer hasn't provided those, you can manipulate the stud to feel where the slot that it moves through is and make your own marks on the rim corresponding with the ends of the slot.
On a car with double-A-arm suspension, the slot would be oriented crosswise (perpendicular to the centerline of the car) to correspond with the arc that the control arm swings through, but if you install Beetle balljoints that way they'll have almost no travel - and you'll have no suspension travel to speak of. The slots must point fore-and-aft on the Beetle (corresponding with the location of the notches on the rim and marks on the control arm).
Here's an example of a balljoint installed wrong - the slot is lined up with the red line on the picture, and it should be lined up with the green one:
Ordinarily the studs stay in place when the old balljoint is pressed out - if a stud pops out of its socket it was ready to fail on the road and you got to it just in the nick of time. The camber eccentric and the upper stud have a taper which locks them together when the nut is tightened, and it almost always takes a press to pull the eccentric back off once it's seated on that taper.
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