I have ridden the Bartram Trail several times to get from Hamburg, PA up to Lake Wynonah, PA. The trail is a great way to connect Auburn to Hamburg, and there are actually a few ways you can connect depending on the type of bike you are riding. Since the bridge near Auburn is not done yet, your best bet to get to the trail would be to use the Reading and Northern Railroad bridge and crossing through the private property as previously mentioned before:
http://www.gmap-pedometer.com/?r=3449695
You can actually get from Auburn to the Trail by using the access road to the state game lands. Bear Creek road turns into the access road and takes you down to a parking lot along the trail, but the road is pretty rocky and a bit more rough than the trail surface so it could be tough on a road bike:
http://www.gmap-pedometer.com/?r=3449699
If you want to get back to the mile or so long stretch of trail from the game lands road you can cross the river at River Road, the signs say the road is closed but the bridge is still there and the right of way is still there too:
http://www.gmap-pedometer.com/?r=3449702
If you want to get from Hamburg over to Kutztown you can hook up with the Livestrong challenge century route that will take you all the way to Skippack:
http://www.mapmyride.com/ride/united...phia/651105237
To get from Hamburg over to Kutztown I think there is a pedestrian bridge just north of the State Street bridge that you can use to cross the river again, the State Street bridge is closed for construction so this ped bridge may be the best option:
http://www.gmap-pedometer.com/?r=3449712
From there you could find some nice back roads to get you over to Virginville then cut south of Kutztown and head over to Lyons and Bowers, the riding in the valley south of Kutztown is fantastic.