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There's a couple of ways to deal with cross members in a fuselage box construction.  Once the sides have bee constructed pin one side down to the building board(pins or magnets) and then pre cut cross members to the size shown on the plans and start on the bottom and glue the cross member to one side.  Then glue the opposite side to the two or three cross members you've glued to the first side.  Holding the opposite side vertical with angles etc.

Usually a box fuselage construction has a straight edge. Where the cross members can be added. Once they have been added you can then add the other cross members in the air. (off the building board)

Second option is to use foam squares/rectangles (made from food trays/boxes) to align the fuselage sides held in place with pieces of masking tape and then to add the cross members, above and below the foam formers.

post #375 shows this process: Click Here

Start the cross members on the straight, parallel sides without taper.  Then pull the tapered sides together (usually at the tail end of the fuselage).
Sky9pilot

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