ok man I'll Try to address everything I can, just let me know if i Leave out anything.
1.)
Atkins I am very anti-atkins, i personally never used it bascially because I know what lack of carbs can do to your body. You'll feel tired, and if you replace it with fats which would make it almost 50%fats that is not good for your body either. so if i were you id stick to the 40/20/20
2.)
Supplements Ok there are two weight loss supplements (w/ the exception of the fantastic wieght loss god of a ECA stack) that I suggest they are Hot Rox or Thermorexin. Hot rox can be bought at dpsnutrition.com for the cheapest you can find it and thermorexin can be found at the afstore.com type this in if they ask for a discount, afdiscount. you might also want to add Tonalin CLA and vitrix. obviously you need the essential protein whey...and listen do not get the creatine.
3.)
Work out ok first off you are going to have to learn to use free weights....and the smith machine does not count. Since you are just starting, it might be a good idea to get started on the machines but you really have to transfer over to free weight bench, squat, deadlift, and stiff leg deadlift. anyway heres a workout plan that I think might be best for your situation.
MONDAY
1.) Bench press (or in your case chest press)- 4 sets 8 reps
2.) Cable Crossovers (or Butterflies)- 3 sets 8 reps
3.) Shoulder press- 3 x 6
4.) Shoulder (vertical) raises- 3 x 10
5.) tricep (arm) extensions- 3 x 8
6.) seated dip- 3 x 8
7.) Abdominal Isolator- 4 x 15
8.) Cardio- I dont think you should do HIIT just yet, wait till you get in better shape. but try this run on a eliptical (the machine where you can like glide or slide) for 20 mins, and try to do this 20:00mins - 18:00 jog 18:00-17:30 run harder, 17:30-15:30 jog. so basically its 2 min jog/ 30 sec run harder do that for 20 mins, if your chest hurts during this stop.
tuesday
1.) squat (horizontal leg press i guess would be the closest thing)- 4 x 8
2.) seated leg curl- 3 x 8
3.) Calf raises- 3 x 10
4.) Lat Pulldowns- first set 12 reps, second set 10 reps, 3rd set 8 reps (looks like this 12, 10, 8)
5.) Arm Curl (?)- 3 x 8
6.) I would say preacher curl but i dont know what other bicep excerices you know/ they have and i am not sure what you mean by arm curl in any case aim for a 8, 6, 4
7.) abs from monday
8.) cardio from monday
wednesday off
thursday do mondays workout
friday do tuesdays workout
saturday and sunday off days...remember you get strong when u rest. I think a MWF might be too much for u right now. and the reason the reps are higher then what i stated is because i didnt know ur stats. You should cut right now, I am about 6'4 345 14% body fat and 42 inch waste, and cutting help me alot.
4.) if you do run in the morning do not run on a empty stomach like someone hear told you. what do u think starts your meatbolism? food! but there is certain food you should eat before working out....FRUIT! liver glycogen is important in fat utilization, so eat a piece of fruit before a workout...remeber not to much tho heres a good link
http://www.parentsurf.com/p/articles/mi_m0KFY/is_7_22/ai_n6170379 as for what carbs to eat after working out i would also suggest a piece of fruit.
i think i answered all ur questions if i didnt let me know