Once I've narrowed down the park/wilderness area to a manageable size, I get to my favorite part of planning. That's choosing the actual route, then calculating mileage, elevation gain/loss, and where needed, choosing campsites.
I'll start by looking at the map, or a specific area of the map, not really trying too hard to discern a route. It really is kind of Zen in that you can't force it, and you have relax and let the map reveal itself to you. It's not too long before i start to see possible routes; loops, lollipops, and connecting circuits really just pop out.
Once this happens, I can take out my notebook, and start jotting down some mileage/elevation figures, sketching each day, and seeing what king of terrain i'm likely to encounter. If the trails I'm looking at are described in a guidebook, I'll read that also.
Between reading these descriptions and looking at the maps, i start to get a remarkably good idea of what each day will be like, and i can begin to visualize the hike, which is always exciting.
Finally, I look at my chosen route, and calculate daily mileage as well as elevation gain/loss.
If I'm hiking in a Wilderness area, such as in Weminuche in Colorado or River of No Return in Idaho, I can leave flexibility in my exact daily itinerary, which i like. In these cases, I'll have a general idea of where I'll be each night, but if i feel like spending a day fishing, or i just wake up feeling lazy, i can adjust accordingly.
However, most National Parks don't allow this practice of "at-large" camping; that is you can't just pick your own campsite and bed down. Instead, when you apply for your backcountry permit, you must indicate your choice of designated backcountry campsites for each night. As a result, there is a lot less flexiblity in planning your route. Of course, I understand the need to manage the backcountry in our National Parks, and this practice certainly makes for a safer stay. And these are backcoutry campsites, so it's not like i'll be next to an RV and parking lot, but still...
You do loose a bit of the sense of freedom that comes with an extended backcountry trip; it is ironic that i have no set schedule for the next 2 months, but I can tell you what campsite i'll be sleeping at from 5/28 to 6/24!
This adds a substantial bit of work to the planning; first, you have to ensure that you apply early enough to get your chosen sites. More importantly, though, you must choose your route to ensure that you have campsite option at or near where you'd want to finish your day. This can result in significant changes to your planned route; a good example of this is in Yellowstone, which i'll get into when i post the hike details for that trip.
Nonetheless, when the planning is finished and the backcountry applications are on their way to the parks (2 months before your trip,) you will have an exact mileage and elevation gain/loss profile for each day of the trip!