Which way to use the reel? Most prefer for a right hander to have the handles on the left side. If you will cast with your right hand, keep the rod in that hand and reel with your left. At least start out that way. You can always change later if you want to. 

Check to make sure your reel is set-up for left hand retrieve by pulling out some line and noticing if the drag engages going out or coming in. It should be ‘on’ when the line is going out. Most reels are convertible to right or left hand retrieve. There should be instructions for changing it with the reel. 

Now as you put the rod together, start with the eyes misaligned and ‘twist’ the sections together. Don’t make it a straight pull; twist them about ninety degrees or so. When you are done make sure they are all nicely in line. This will seat them properly. Check the sections often to make sure they still have some paraffin; it can wear off over a season.

Presuming you already have the line on the reel, put the butt of the rod on the ground and after folding a small loop in the fly line, start poking it up through the guides. Don't put the line through the tiny little loop right by the cork, that's a hook keeper.