I am not familiar with DMP6050, but after quickly reviewing your library, "helper_3d_mat.h", it appears to have a class called "Quaternion" that will certainly clash with Quaternion in the Eigen library. Since the "helper_3d_mat.h" only has 276 lines, I recommend changing the name of the class in question, but you'll have to rename the instances in DMP6050. Also, you have to leave the line "using namespace Eigen", otherwise you'll have to type "Eigen::" as a prefix to Eigen related commands. See the following example:
http://forum.arduino.cc/index.php?topic=144446.msg1089371#msg1089371
Good luck.