The title pretty much says it all. I've been nesting a smaller copy of the hull inside the main version and using a subtract boole to cut out circles and lines, but the results are slow to load and don't look that great. I'm wondering if there's a simple way to just cut them directly out of the hull without resorting to vast amounts of nested booleans.
If the panel lines do not run parallel the mesh I am always using boolean cuts. First I detach the polygons that will be cut off the rest of the mesh. Then I try to reduce them by using symmetries and instances as much as I can. I do cut two parallel panel lines and after cleaning up I extrude/bevel the polygons between them.
I've only been doing this a few months, so I'm not really that up to spec on a lot of the how to and wherefores. Might need a bit more of a runthrough here.
I've been uising Cinema 4d since 1999 (holy crap, has it been that long!) and i'm still learning new techniques, so if you've got any questions I'll be more than happy to help and if I can't I'm sure somebody else around here can (looks in Nightfevers direction and runs haha).
Then I use the bool tool to cut those lines in to the polygons from the main mesh, clean it up then just bevel that single line to prefered width and then extrude it down and then you have your custom panel lines.
This way do include some cleaning up before and after you extrude you lines, but if disconnect the polygons from the main object first it becomes much easier.
EDIT: The panel lines below on the wing and the main hull of my Halo Longsword model was done this way, it's not very clean and it takes a few min to clean the polygons afterwards, but it was the easiest way I could find to get the lines just the way I want without using the knife tool and cutting a lot of unneeded lines.