In general caps are generic. Once you drag it on to the sketch, then Inspector (lower right pane) will let you select things like value, voltage, and package. From the 3.5mm I'm guessing the cap is smd because that isn't a standard through hole spacing. So you need to know what package it is 0405, 605, 0807 to get the correct footprint. Then you can either look at it in pcb or better, file->export->for p[roduction->gerber as a gerber (which is what the fab house will make the board from) and check there what the spacing is. For the bom, set the part number field in inspector to the correct part number.
Peter