The present invention is directed to balloon folding configurations and methods for catheter devices having dual lumens in radial proximity to the balloon, such as, but not limited to, self-aligning stent delivery systems for treatment of bifurcated lesions. The configuration designs alters the conventional catheter profile by packing balloon materials in otherwise vacant areas located on both sides of the side branch shaft and/or the parent shaft, such that the device takes on more of a round profile instead of the classical elongated egg-shaped profile.