Find the one that is on a larger diameter line that goes from the firewall to the compressor directly. Better yet, look at the two tubes/hoses that are connected to the compressor as a reference. There are a total of three refrigerant hoses under your hood, so a brief explanation is needed.
One line, usually a smaller diameter, will go forward from the compressor connection to the condenser coil mounted in front of the radiator. A second smaller diameter line will run directly from the condenser to the firewall. This one is NOT conencted to the compressor. These lines are usually 1/2" or 5/8" diameter. The lines are both on the high pressure side of the system, so DON'T connect to those.
The third tube/hose should run directly back to the firewall, and is usually 3/4" outside diameter, or so. The line may be connected to a silver cylinder (receiver) that is mounted directly at the heater/evaporator housing. Look for a tap on this cylinder, too. It is usually under a plastic cap, if there. There is one on the newer GM units. That's the suction or low pressure line connection. Hook your valve hose to that one.
It is possible that the 1/4" fitting you described is on the suction connection at the compressor. If you check out the hose routing as described above, you can decide which fitting to use.
The older cars all had 1/4" SAE flare fittings on both lines, so it's easy to mix them up if you haven't done refirgeration work before. The newer R-134a systems and conversion kits use different size fittings so you can't mix them up. That's what you saw with the different sizes you referred to.