It is normal for a system that is low or out of refrigerant, for the compressor to cycle briefly as you described. As the system fills up, the compressor will run for increasingly longer times until it runs pretty much continuously when fully charged.
As Fuddy said, make sure the AC is on high. I find that filling on the suction side when sitting can be a very slow process, but if you wire up the can in a safe spot in the engine compartment, so that you can close the hood and drive the car, the air forced through the condenser will allow the system to operate much more efficiently and it will take the charge much more quickly. You can tell when the can is empty by feeling near the bottom, if it is still cold, there is some left. If warm, it'* all gone and time for the next one. On a warm day, you can charge a 12oz can of 134a in about 4-5 minutes at 50 mph.
If the system was opened, it will need to be evacuated by pulling a good (29"+) vacuum for 45 minutes to remove moisture before you recharge. You may want to consider changing the receiver/dryer if the system was open to the atmosphere for a significant length of time, especially under humid conditions. AC systems cannot tolerate humidity at all.
It is safest to have the system evacuated before you recharge it. That way you can keep track of exactly how much refrigerant you put in so that you don't overcharge it.
Don't forget to put an oil charge in to replace what leaked out before repairs, or you can destroy your compressor.