Quilter needs a complete schematic and a board outline from your ECAD tool (Altium, Cadence Allegro & OrCAD, Siemens Xpedition, or KiCAD). The board file should include the board outline, mounting holes, connectors, and any other mechanically critical components already placed. Anything inside the board outline is treated as locked. Anything outside is what Quilter will place for you.
For better outputs, include rooms or placement regions to guide the floor plan, set your stackup and DRC rules, and use net classes to flag power nets and differential pairs.