First, I want to make sure we are comparing apples to apples. My trailers Have the wheels/fenders on the outside of the frame rails. I hope this is what you intend by the term "deck over"".
You have your choice of turning the channel with the flanges inward or outward. They both have their advantages and disadvantages. With the flanges out, this will protect the marker lights from getting knocked into, but it makes it more difficult to wire because you have to run conduits or wire supports inside the frame to support the wireing. With the flanges in, you actually have a space between the flange and the edge of the lumber, as long as you make the lumber the same height as the frame. You lower the cross members the same thickness as you wood. This way you have about 1.24" space to run your wireing the full length of your frame, makes it a lot easier to wire. While I am on the subject of wireing, I dont like to use conduit. I like all my wiring exposed so I can easily make repairs. I live in Michigan, so I know I will be making repairs. The road salt is hard on the wireing system. I know people will flame me, but putting the wire in conduits does not make the wire last longer. It just makes it a ***** to repair. I like to keep it simple. Do not buy a prefab trailer wire harness. Make your own with a decent stranded 14awg. I like to strip the wires, twist, solder, roofing tar then a wire nut. This recipe has been the best I have found so far. My trailer is on it's 5th winter and I have yet to make any repairs or change lights (LED's).
As for mounting the axles to the channel, just weld the spring hangers to the bottom of the channell flange. You are going to find out that the flange is narrower than the spring hanger. This poses no problem, the channell is plenty strong. While we are talking about welding the hangers to the frame, I like to just weld the front and back of the hangers. I dont weld along the sides. With the 3 hangers per side, if you weld the sides, the welds will pull on the channell as the welds cool and shrink. This will make the trailer front and back look like it is sagging if you look at it from the side at a distance.
If you are willing to send me an email adress I will send some pictures of a trailer I did last month. You will be able see a lot because the photos are of the trailer in the construction phase.