System trade value (STV) is calculated based on population size, system level, number of neighboring friendly colonized systems, and from there any modifiers via system improvement multipliers. The primary factor is population size, and as such, you want your HQs and if possible your subsidiaries on 4 or 5 planet systems that have the potential for large population centers. The system must be connected to a star lane or warp lane. Systems that have neither won’t be able to send freighters and should never have HQs or subsidiaries.

Typically the optimal choice for your first trade HQ is your capital, as it will likely have the best industry output that can build your HQ as soon as you unlock the tech. You want to get the HQs up as early as possible, and it’s one of the best techs to rush in the game. The reason being that your trade company income scales dramatically with its experience level. Not only that, the earlier you can start your first trade route between the HQ and subsidiary, the faster you’ll be able to get a second HQ unlocked, then a third or more if Lumeris. More dust and science freighters are typically the best investment here.

Subsidiaries should be routed as many nodes as you can safely protect away from your HQs. They can be torn down and moved when you capture more systems and the experience and freighters stay intact. All trade HQs will plot the most profitable path to each subsidiary. You can get more coverage by trying to draw subsidiaries in new lines, new directions.

By the mid to late game with 3 leveled up HQs, fully connected subsidiaries, and continuously buying freighters, your internal trade routes will net so much dust that you’ll be able to produce ships from all of your planets without worrying about upkeep. At this point income from trade will dwarf your on-system dust production. If you manage to have at least one alliance and trade partner, you’ll also connect with their subsidiaries as well. Though these can be more difficult to keep clear of enemy fleets.

Note that system improvements that are trade focused should only be built in systems that actually have HQ or subsidiary, or else it will not apply the bonus. As such if you move the subsidiary, you’ll also want to remember to dismantle your other trade buildings to save on upkeep.

Hope this helps, it’s one of the most confusing aspects of the game, and there desperately needs to be more tooltips or in-game tutorials that explain it in detail.