There are a lot of different exercises you can do to increase your horse's fitness level that doesn't involve hills. I love this book:
It has punch-out cards for each exercise that I ended up getting laminated so that I can plan out a few exercises before I leave my house and bring them with me to the barn. It also has some great detailed plans on how/when to utilize the exercises.
I also just started a thread called "New to Eventing - Tips/Advice" where there is a suggestion for building up endurance to navigate a beginner course.