You 'can' delete unseen polygons. It might cause holes on edges, etc. I sometimes keep edges like that to keep the model looking good.
If you have polygons on the back sides, then those will need area's in your texture sheet as well. A texture for the exterior and one for the interior, and if they are the same part, you can squeeze them into the same sheet.
By the way. You can screenshot the UVW layout and paste that into a PSD (layered graphics file) as a home made template. Use Wand to delete the area's around parts in the Template. Then you can 'select' that layer and its selects the objects (islands) in that layer and you can then use paint bucket to Fill zones, (fast and easy).
Once you have your 'template' that Lithium produces (ha ha) you then move that into Photoshop or Gimp and create your bitmap graphics. But, do that in layers, like a PSD file, and keep the master PSD and burn (Save As...) copies into BMP format to use in the sim.
A technique I use is get the template into PS, copy the template layer and hide one so you have a backup, then use Wand tool and highlight the blue background area on the visible Template layer and delete that. You now have the parts left over (area's) that are the parts of your boat. Paint them a color on a new layer and name that 'base color layer' or something to that effect. I always (always) select those areas and raise them (increase them) by 3 pixels to keep edges from having no color in the sim. Then later, get some awesome wood textures from online and start using those to create your wood hull graphics (on new layers). Never compress or collapse the layers. Make 'Save As...' copies into BMP from your layered graphics.
Also, keep adding parts to your texture sheet. You can add the material to another part, map it, and you will see the areas' still open in the graphics where you can place new small parts to fit in the left open zones. Use every inch you can on your master sheets.
Also, as a small note and a tip, you can save your templates with their lines of mesh and use those to align with later (like door lines, panel lines, etc) but turning on and off layers (for visibility) and making your edge lights, moving parts around, etc, etc. Helps out. Dont delete your templates in your layers (unless you redo them).