These are my observations and opinions as the result of 22 years at Philmont, include a year on staff as manager of logistics.
Vaca -- not a very good starting camp, but it doesn't make much difference on this day.
Ute Springs -- you will hike up through Harlan. Good program available. Then hike around the mesa to Ute Springs camp. Most of the campsites are in a gully to the right of the road, along a (usually) dry streambed. There are some dustier and poorer sites up along the road. If the stream is dry or nearly so, there is a weak and unreliable spring in the middle of the camp near the stream bed. Otherwise we usually use the stream that comes down Grouse Canyon, off the road to the left. The commissary is up the road and on a side road spur. About a half hour hike away from camp.
Cyphers Mine -- Leaving Ute Springs, take the Grouse Canyon trail to the head of Cimarroncito Meadow. You can go through Aspen Springs camp but it is longer and I don't think as pretty. Go down Cito meadow to the staff cabins and take the program. From there continue down the meadow to the Hunting Lodge. Across the nearby road is the trail up to Cyphers. Near Lamberts Mine (nothing there anymore) you will go around a ridge to Cyphers. There you will stay in Adarondak Cabins as the ground is too steep and rocky for tents.
Comanche Peak-- A long and fairly steep climb up a new trail to Thunder Ridge then on to the top of Comanche (dry, your last water until the next day is from Cyphers to plan carefully).
Clear Creek -- cross Phillips and go down the west side to Clear Creek. Good views and a fairly easy trail after what you went through yesterday.
Crooked Creek -- From upper Porcupine camp you will turn left up onto a meadow. This is Crooked Creek. A good camp and an easy hike from Clear Creek.
Beaubien -- Go back to Porcupine and follow the creek down to Phillips Junction Commissary. If you have an early start from Crooked Creek, I would ask to leave packs at the commissary, take raincoats and stuff and side hike to Fish Camp. The kids always find it interesting and it is an easy hike down and back. Back at the commissary, draw your food and hike up to Beaubien--also a fairly easy hike, but you are now heavy with food.
Lay day at Beaubien -- my favorite layover side hike is to Black Mt. Camp. It is a pretty camp, easy hike and good program. It takes a half day round trip.
Bear Caves -- You can take the new (may not be on the map) trail out of the back of Beaubien Camp that parallels Bonita Meadow in the woods on the south side. It intersects the trail going over Webster Pass. Turn left to the meadow and across Fowler Pass on the other side. Drop down to Crate Lake. You can take the lumbering program there. It is then less than an hour up to Bear Caves. The camp is swampy and has a lot of mosquitos. Few good sites but there is reliable water.
Urraca -- continue around the side of Fowler Mesa until you see the trail down to Stonewall Pass leaving to your left. Another new trail that wasn't on the map last year. Be careful. From Stonewall Pass head up the road that goes to the top of Uracca Mesa. Follow the top of the mesa to the east and take the trail down to Uracca on the north side. Good program and campsites.
Base Camp -- There are several routes to base camp. The most popular is to drop down to Rocky Mt. Scout camp near the stockade. Then cross the meadow towards Tooth Ridge, aiming just to the right of the Tooth. There is a meadow trail heading up onto the ridge (a trail from the stockade just to the right of the Tooth is steeper and more difficult). The meadow trail is as tough a climb as you will have on this route. At the top of the ridge you will meet the ridge trail. You can hide your pack nearby and to west to the Tooth. It is a short side hike to the tooth. Go back and get your packs and follow the top of the ridge back down to base camp.
An easier way to base camp, if you are pooped by now or in a hurry, is to take a meadow trail around the base of tooth ridge to camp. This is a boring hike but gets you back quickly and more easily.
Good luck. Lots of side hike opportunities and good program available. Get up very early and you have a chance to get most of them without driving everyone in the ground with fast hiking.