Newbie looking for advice.

Hello, I posted a little about my self in the introduce your self thread but here it goes a little more.
I'm 34 y/o 5'9" and 162(+-) lbs My body shape is skinny all around I have thin puny bones and a funny fast food and beer belly.
At my 34 I have decied to get in shape, I have 3 small ones that need me arround and in shape to keep up. I have never been the sporty kind of guy by the contrary all the sports I do are fairlly laid back (hand gliding, skydiving, scuba, motorcycles) I'm station at Fort Jackson for the next 5 weeks with a gym down the block ( no excuse not to go) I want to copy some training regimen from your site for me to do but here is my problem:
1- Overtrain = we do PT (physical exercise) 3 days a week  M, W, F, 2 are runing ( 2 mile, 4 mile)  1 is muscle failure (push ups, sit ups, flutter kicks)
2- Diet = the food here is like poison, can't say is nutricious at all, would have to relly heavilly on supplements (suggest please)
 
What would you suggest I can do for training looking at both my concerns.
 
Thanks in advance for all your help, I will post more since I'm sure some other doubts will come to mind.