Just copy us. We do it smarter on this issue, quite frankly.
Like the United States, the Australian Commonwealth is a federation of multiple states with a capital that exists within a separate territory distinct from all the states (Australian Capital Territory = District of Columbia but with a slightly more powerful government). The reasons in our case are essentially rooted in historical Sydney-Melbourne rivalry but the result is the same for comparative politics purposes.
We also, like America, have a variety of overseas possessions, territories such as Norfolk Island, the Antarctic territory, Christmas Island, the Cocos and Keeling Islands and, formerly, New Guinea, which are also considered territories within the Commonwealth.
What we have is a two tier system that gives territories different statuses -- Internal Territories and External Territories. The two internal territories are the ACT and the Northern Territory. ACT is an exact analogue to DC while the Northern Territory is simply an area that never attained statehood and is relatively sparsely populated. For most purposes they're both undifferentiated from the states, citizens pay taxes like normal, most functions provided by states are also provided by the two territorial governments (education, health, road laws, etcetera) or in some cases the federal government (the Australian Federal Police).
These two internal territories have members of parliament and their own governments which have less power than State Governments (most significantly, legislation can be vetoed by the Commonwealth as has happened with euthanasia legalisation in NT and same sex civil unions in the ACT). In the House of Representatives the rules for parliamentary representation are the same as for states - one district per X number of voters, districts have to be drawn to make socio-geographical sense. In the Senate each state has only two Senators rather than the 12 all the states have.
Norfolk Island, Christmas Island etcetera are defined as external territories with drastically less autonomy and voting rights and so forth. Even within these, there are differences as with the different colonial nonstates of the USA. Norfolk Island is the only territory with self-governance (and I think mainlanders need their passport to enter and don't have right of residence) while other territories are rolled into a parliamentary electoral district in the House of Reps.
It would be incredibly easy to simply define DC as an "Internal Territory" as distinct from all the external ones, and thereby entirely avoid the whole "why not Puerto Rico, Guam, Samoa etcetera?" problem as well as ending the farcical and anachronistic status quo which treats your own capital pretty much like a colonial possession.
