1) Is it common not to be able to start the generator if the motor isn't running?
No. This suggests a weak battery or perhaps a poor (corroded) connection between the genset starter motor and the battery. Most likely your genset is started by the chassis (engine) battery rather than the house batteries, but this is not always true.
2) When the motor is running I can only start the generator from outside, the toggle switch inside on the control panel seems to try to start the generator but can't quite get it to go on and once started from outside, when trying to shut it down from inside it tries but can't quite get it to shut off either, why?
Can you describe what happens when you use the remote switch? Does the genset starter crank at all? Maybe just "click"? Click and grunt once? Do nothing?
3) When checking the battery condition from the control panel the led lights indicate the batteries are good but how do you know that both the deep cycle batteries are fully charged? won't the control panel only be referencing the main starter battery?
Most likely the control panel lights monitor the house batteries rather than the chassis battery. However, when on shore power or with the genset running, the monitor is probably seeing the charge induced by your built-in battery charger rather than the true battery state. I would not have a lot of faith in that monitor anyway - they tend to show "good" until the moment before go completely bad. I suggest you disconnect the RV from shore power and leave genset and engine off. Turn on a couple of interior lights for an hour and then check the house batteries directly with a voltmeter. The voltage should be 12.6. or very close to it. Less than 12.5 would indicate at least one weak battery. More than 12.7 indicates there is still a surface charge and you need to put an additional load (more lights, etc) before you can see the true state. 13.0 or more indicates you still have a charger attached somehow.
You can also check the individual cells of the batteries with a hygrometer (specific gravity tester). These are available in any auto parts store/department and are inexpensive.
4) lastly, the air bags are only on the front springs and I found where to inflate them, it was on the bottom of each helper spring. My question is how much psi should be in each bag and how often should you check and adjust the amount?
The amount of pressure depends on the front axle weight capacity and your preference for ride & handling. The minimum is 50 psi and the max is 90 psi (unless you have upgraded to the new heavy duty bags from Workhorse, in which case it is 110 psi). Above 50 psi you can apply your own preference for handling and ride comfort. More pressure yields somewhat more responsive steering/handling at the expense of a firmer ride. I'm guessing a Flair is on the 14,000 lb GVWR chassis, in which case 50-60 psi is probably about right. The heavier GVWR chassis usually need 70 psi or more.
Check the bag pressure again in a week and then at one month. If it stays as initially set, I would check it maybe twice a year or if handling deteriorates. If it has gone down any at all (after allowing for temperature change) I would check it often. Don't drive the rig if the pressure is below 50 psi. Replacing leaking bags is not terribly expensive and can be done yourself.