Yes, this is a great ride and well-supported. I rode the 50 during the 1st year that I was riding and they didn't have the northern loop yet. There were rolling hills (Chuckanut Drive) and alongside the lake, but nothing too hard. The Bow-Edison section is flat and you could experience the head and crosswinds out on the Skagit flats but it's a beautiful route whichever direction you choose.

I've done plenty of rides and loops in the area over the years since and think that I'd agree with smittykitty in that the northern loop may be the less hilly option. Also, there are shorter loops in case you get there and want to ride, then opt for less than 50 miles.

No, you don't have to ride a full 50 before that day; if you consider it your goal ride then increase your mileage a bit each week to where you're closing in on 50 and so that it won't be much of a stretch on that day, if you haven't actually done a 50 mile ride yet.

If you live up in Whatcom county or are somewhere near Bellingham, maybe consider going on a few of the Mt Baker cycling club's group rides beforehand? That way you'd get some group riding in and maybe even an advance experience riding on some of the same roads that'll be used in September.
bonus: Boundary Bay Brewery is at the finish! IMHO!