You have a number of questions so let's take them one-at-a-time.

Booking through Contour is fine - you will still get skymiles and MQMs unless you company has negotiated special rates. Special rates can lower the mileage awarded - but most companies use Concur to manage travel expense information without specially negotiated rates - you should be fine. If you want to confirm see if the prices shown on Concur match the prices available on Delta.

As to how much credit you will get - that depends on the class and the operating airline. If you are flying on Delta metal you will get normal mileage credit even though you booked on Concur unless you book an "E" class ticket.

If you fly on another Skyteam airline and want to credit the flight to Delta - add your Skymiles number to Concur (which will then insert your number into your record). How many miles you get depends on the airline and the class you fly. The Delta website lists each partner airline and the credit you get for each fare class on each partner airline.

As for upgrades, if you are flying Delta metal, the flight will show up on the Delta website along with any other flights you have pending. You have the same upgrade opportunities you would have if you had bought directly from Delta (remember to avoid E class if you want upgraees).. If you are flying partner airlines check the partner as to how they treat Delta flyers. If you are Diamond you will likely be classified as Elite Plus which means a shot at upgrades but on some partners (Alaska for example) the chances are not great.