Use whatever is more convenient for you. It doesn't matter what units packages are defined in because any decent software decouples package definitions from layout and routing dimensions anyway. Use whatever metrics the datasheet uses when defining the package footprint, since that will minimize errors. Even then, I switch back to inches when defining the silkscree and documentation layers because that's what I can relate to more directly.
For layout and routing, use whatever you are comfortable with. I learned this stuff thinking in inches and mils, so that's what I use. I can picture 8 mils in my head, but I'd have to convert the equivalent in mm to get a mental picture. That's what computers are for. They are very good at multiplying or dividing by 25.4, so let them serve you, not the other way around.
When exporting files to a board house, I'd use inches. That seems to be more of the univeral standard, probably due to history. The board house's computers can multiply by 25.4 too, so those board houses that use mm internally won't be bothered. A few years back, some board houses wanted all input in inches, but I suspect that's no longer true today.