The first step is to insert your tube into your box. This will require cutting two ellipsoid-shaped holes in the box so that the tube is held at an angle.
Squeeze your tube slightly into an oval, trace this outline on the top of your box.
Cut out this hole in the top.
Insert tube at an angle and trace out a much longer oval in the bottom of the box.
Cut out the oval.
Widen and lengthen holes as necessary. It may take a couple revisions to get the length and width of the second hole correct.
Push tube through both holes. The fit should be tight, but not so tight that it bends the cardboard tube or distorts the box dramatically.
If you don't have an X-acto knife or similar, the 3D printed handle pictured in this guide can be found on Thingiverse and pairs well with standard utility knife blades to make an excellent hobby knife.