My wife and I have been backpacking together for more than twenty years, mostly weekends and some week-long trips. Nothing over 75 or 80 miles. This summer we did our first long hike together, the Long Trail in Vermont, which is about 275 miles. So she had a lot of backpacking experience, but very limited thru-hiking experience, like hitching and resupplying and all that.
We spent 27 days on the trail, 24 hours a day, never more than a few yards from each other. We LOVED it. Being able to have that kind of one-on-one time, without any of the distractions of modern life, was an amazing gift.
Of course there are challenges. We were lucky in that when one of us was having a bad morning, the other one was in pretty good shape and could offer support. We also rallied as a team against a common enemy -- the trail itself. (Gah. #$%#$%%$ Long Trail. I think I set a record for f-bombs in one month.)
Some thoughts:
Get experience hiking with your gear, setting up camp, etc. It doesn't take long to get into a routine, but it helps if you already have some idea how to pack your own pack, how you both will split up camp chores, whether you like to eat the same things, etc. When we get to camp, my wife goes to the water source and fills our water bags, while I set up the tent. Then she sets up all of our sleeping gear inside the tent while I filter water and start dinner. The end result is a nice campsite and dinner, all at about the same time. In the morning I get up and go get our food bags to start coffee and breakfast while she packs all the sleeping gear and starts tossing stuff sacks out of the tent. Then we pack up and sit down for breakfast.
On the AT I would suggest that you be willing to hike apart when necessary, but I don't know if that's a good idea on the IAT.
Give each other some space when needed.
Give some thought ahead of time to what each of you will do if one or the other decides to get off the trail. Keep hiking, with support from the other person? Get off the trail as well?
Also think about hiking style and how that affects both of you. If one of you is a "get up at 5am and hike fast all day" type of hiker, and the other is a "sleep until 9 and stop at every overlook" type, that's something to work out in advance. You probably don't know what kind of hiker you are, yet, but you can think about how goal oriented you are, and how you handle challenges and work with other people out in the world.
Thru-hiking is work, and it's frankly harder than my regular job. Way harder. There are plenty of times when it's not really much fun, too. But the good parts are REALLY good, and what I remember when I'm finished is the views from all the mountains that I climbed, and the way the light looked slanting across the pond at sunset, and the feeling of exhileration during a storm, and the cool air blowing across my face at night. It also makes me appreciate all the little things that I ignore in the modern world. Like showers, and pizza, and cold beer, preferably all at the same time
Good luck.
This is a way to get to know someone else on a fundamental level, deeper than you ever thought possible.