I've put together a unit but only when I've already started enveloping it have I realised that on the shoulder there are two duplicate polygons. Is there a way to remove them without affecting the resh of my mesh?

Yep, just select and delete the duplicate polygons.

I can't seem to delete them without deleting the polygons I want to keep though. I must be selecting them wrong.

Tell us more about what you're doing and post some screenshots if you're still having trouble.

At the moment, I'm using the polygon selection tool, but you have to drag that over an area to select polygons. Obviously in so doing I'm also selecting the polygons I want to keep as well.

Use the raycast polygon selection tool, press the U key to enable it and you'll be able to click on and select individual polygons.

Thanks for explaining that to me. I got it solved now