The cleanest approach is to treat the Grid Boss the same way you would a backup/critical-loads panel. Pick the 200 A panel you’ll route through it, then move only the backed-up circuits into that panel and leave non-backed-up circuits on the other. That keeps your backup loads isolated, avoids overloading the inverter during outages, and keeps wiring simple. A separate critical-loads panel also works, but since you already have two mains, using one as the backed-up panel is usually the easiest.