Participatory budgeting is a democratic process for allocating funds to projects based on the votes of members of the community. However, most input methods of voters' preferences prevent the voters from expressing complex relationships among projects, leading to outcomes that do not reflect their preferences well enough. In this paper, we propose an input method that begins to address this challenge, by allowing participants to express substitutes over projects. Then, we extend a known aggregation mechanism from the literature (Rule X) to handle substitute projects. We prove that our extended rule preserves proportionality under natural conditions, and show empirically that it obtains substantially more welfare than the original mechanism on instances with substitutes.