i haven't played HRE, but most factions are best with a city to castle ratio of at least 3:1, then you make sure the cities use their free upkeep militia for garrisons, and only use a limited number of field armies to fight your battles. this has the biggest impact on upkeep costs
in terms of building the economy, build roads, at least the first two levels farms, ports and markets in cities, early on. in the early game, i even minimise taxes to boost growth so that when i actually do go a-conquering, my economy can support it.
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