The optimization of trajectories with a finite number of branches is considered. The conditions of the Pontryagin maximum principle are written down in a general form for such problems. A technique for reducing the boundary value problem by transferring the conditions from right ends of side branches to the main branch is presented. The features of the through optimization of trajectories of space transportation systems with constraints on the landing/dropping areas of spent parts are described. Methods are given for taking into account safety requirements for stage separation, which impose control constraints on the main and side branches simultaneously. For this case, two models of the separation process are proposed: with integrated consideration of the change in the phase vector and a model of a frozen jet. Specific optimization problems for air launch projects are stated.