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Personally, I'd stick with defining a nation as a geographic region, and potentially link that to individuals who are members of that nation. You could do that either through express linkage to the corresponding topic, or by using tags to define an individual's nationality.
I've always conceived of political groups and factions as groups more focused on a particular issue within something like a nation. For instance powerful mercantile guilds, or political parties, or revolutionary groups - that sort of thing.
That all comes down to my own way of thinking about world building - I tend to divide up physical geography pretty rigidly and hierarchically (towns are contained by counties, are contained by states, are contained by the nation, for instance), and I tend to organize people more with linkage and tags since people can move between geography fairly easily. If I had a character that I was pretty sure wouldn't be encountered anywhere else, I may contain them in a geographic location (a shop owner in a town, for instance), but typically I would just add their information as snippets to the location itself (e.g., define the shop contained in the town, then detail the owner in the shop topic).
But, over all, the fact that there is no one single way to do anything is part of what makes Realm Works so great. It does make it a little overwhelming to start, but the program is incredibly adaptable to whatever organization system works best for you. I would suggest taking a little time to really think about how you want to organize stuff, and once you have a method stick with it (at least within a single realm). This is why building a few practice realms is a really good idea - maybe pull out some old adventures or supplements and start entering data to experiment with different ideas.
Regardless, welcome to the community - Realm Works takes some time to learn, but I can't imagine DMing without it now.
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