generally you need a solid rod (same size as the inner diameter of the barrel - no significant gap) to push into the barrel as you pull the cylinder out - this keeps the springs from flying everywhere. you start by putting the key in and turning it - this brings the pins with the cylinder and leaves the 'top' pins with the springs - yes there are generally 2 sets of pins in each slot - the top pins are flat and keep the springs from getting caught in the cylinder when it rotates. in the case of master pins (sometimes used for valet keys), they are also flat pins
i have not looked at the pins for the Pebra keys and do not know their sizes compared to house lock or other car lock pins. but if you get the cylinder out, you can put a different key into the cylinder and place or rearrange the pins to fit flush with the cylinder. if they do not fit exactly (stand proud), you can file the pins down slightly ... if they don't reach the top of the cylinder, you will have a problem of the cylinder not unlocking.
when you re-insert the cylinder into the barrel, again, put it in rotated so the springs don't pop into the other slots
if you do send springs and top pins flying, using a long pair of tweezers, insert the spring into the barrel, followed by the top pin - holding it down while inserting the rod (just to cover that slot), then repeat at the next slot. you need to be careful with the pebra keys as there are pins on both sides of the key which makes things more difficult.