Well, in the play calling screen you should be able to use the right thumb stick to cycle through various formation packages. There should always be a package called "Backup QB" or "QB2" or something like that. That's all you really have to do.
In the NY Jets playbook here are some good plays:
Gun - Empty Trey
This isn't a run for your QB, but a good set up play for:
The normal Jet Sweep is what should keep the D honest.
You also have a Run/Pass option with:
I recommend you flip these plays because Webb is right handed and you want the play to flow to his strength. You want each play to look the same until that last second to fool the D. Just because Webb is in the game doesn't mean it has to be a QB run
The same formation also has:
Anytime you play with an empty backfield out of the gun, your QB can be a running threat. You spread the D out both horizontally with the formation and vertically with the routes your receivers run. This can create running lanes for your QB.
Obviously the Shotgun - Jet Heavy is nice as well:
This final Play Action, the QB fakes his the QB blast and then backs up for the pass... which you can still choose to run out of.
Out of the Shotgun - Split Jet you get these nice plays:
Flip the play for your right handed QB, and at the snap you can hold the sprint button and flow with the play action and run to the right. It's a good option to dump it off to the back on the sideline, look for a receiver over the middle deep, or just take off. Three good options... and don't be afraid to just throw it away.
Slip Screens are always good and easy to complete. There are also two nice run plays, the Draw and Power O. Again, the goal is to keep the D honest, especially if you are playing against a human opponent. You don't want them to see Webb and think "Oh, it's a QB run"
This Mesh play is also nice. You have short options, but can also run to the same side as the HB Wheel route [remember to flip the play] and if the D bites on you, throw the deep pass. If they try to contain the HB, take off with Webb.
Next, out of the Shotgun - Trey Open formation, you have:
Which works well in conjunction with:
Then for the QB run you have:
and...
If you hold the A [X for PS3] button, you will hand it off to your HB on both the Read Option and QB Wrap. If you don't, the QB will keep it.
Also there is:
Again, after flipping it for Webb, you can take off to the right, stop and throw it back across the field to your HB, or as you roll, you will have all of your other receiving threats running routes at different depths to the right with you.
Combined with a HB slip screen and a number of other good passing plays to choose from, these are great shot gun formations to use with Webb.
That's 18+ plays [not all QB runs, but still] that should work very well for you. An average NFL game has about 120 offensive plays [about 60 for each team.] Those plays I showed you can quickly and easily make up about 1/3 of your offense. The Jets playbook also has the Wildcat, although I don't care much for the Wildcat. In Madden the D sells out on runs from the WC. They don't respect the fact that it could be a pass, because the AI knows it isn't a pass. That's why I use play action passes as a fun way to simulate the option play.
I hope all of that helps you enjoy the game a lot more.