I assume you are talking the two idle mixture screws towards the bottom of the carburetor. First of all they do not effect the timing in any way. That being said, it can be tough to set the timing unless the idle adjustment is in the correct ballpark. The initial setting for these screws is 1 1/2 turns out. To set this, turn them in until they seat. Do not be too aggressive with this, just turn them in until they stop, then back them out 1 1/2 turns. Set the idle speed screw on the main carburetor linkage so that it contacts the stop. Try to start the car. If it will not idle, screw in the idle adjustment screw until it does. Once you get a reasonable resemblance of an idle, it is time to set the timing. Disconnect the vacuum advance line from the back of the carburetor. Find an appropriate sized bolt bolt or brass plug to fit the vacuum port in the carburetor and screw it in to block the port. DO NOT screw it in tightly as you can damage the threads in the carburetor. Using a timing light, turn the distributor so the light flashes when the pointer on the engine lines up with the bump on the front pulley. Once you have that, tighten the distributor hold down/ You may have to do this once or twice, because the distributor sometimes moves a little bit when being tightened down.
Once you have this down, remove the bolt from the back of the carburetor and reconnect the vacuum advance line. Now it is time to set the carburetor. screw one idle screw in until the engine starts to stumble; then back it out just a little. Adjust the idle speed screw to get the idle close to the idle speed specification (this is around 500 RPM for most stock flatheads). Repeat this exercise with the idle screw on the other side of the carburetor. You may have to go back and forth a time or two until you get it right.
This should result in a smooth idling engine. If you can't get it, there is probably something else wrong. Check the compression and make sure the carb is squeaky clean. Sometimes, there can be ignition problems (bad coil, burned points or plugs, etc.). The best solution to this is to make sure you have all of the best components installed properly. Good Luck.