All my +6 skycube textures are at 6144x1024. What I am wondering is does the engine split this into the six 1024x1024 properly and that I should not worry about hitting and texture size limits on peoples graphics cards?

The engine does not split textures. For this reason, when you have a huge texture, use a DDS image with one additional mipmap. This way the people with texture limits below 8192 can also see your sky cube, although with half resolution.

This is quite unfortunate as .dds is not as good quality. As well, half of my textures resolution still wouldn't be supported on old graphics cards. I don't know why we have to use a +6 texture anyways... as it's a waste of space and resolution. Other engines make skycubes comprised from individual images. This is much easier to do the art for too.