How do you safely charge the battery in a 98 e300d?

[83w126]

I am pretty sure there is air in the fuel lines because it wouldn’t start after sitting in the driveway over night. It was running before though, so I rolled it out in the street and have been trying to get it started, but the battery is starting to die. I am not sure what to do now, because if I understand correctly, either charging the battery with it connected or leaving it out of the car for too long will cause all kinds of other problems (reprogramming keys, potentially triggering the anti theft system, etc).
I am really kinda frustrated, I spent $5k on this car and only put about 900 miles on it, and now I don't think I have the skill to get it running again, and I don’t have thousands of dollars to throw at a shop, so I am likely going to have to sell it as a parts car and lose several thousand dollars. I probably should have kept my 300SD, it wasn't that great either, but at least it always stayed running.