For what to do if the Faction Manager of Yamatai disappears, see Faction Will for Yamatai.
In general, FM Wes is highly active and responds quickly to requests involving Yamatai. All RP that includes Yamataian government personnel, including and especially those of the Star Army of Yamatai, should be discussed with Wes in advance.
NPC portrayal individual Yamataian citizens does not require FM approval, but the appearance of large groups of citizens may. When in doubt, ask Wes.
Yamatai doesn't mind if Nepleslian and Lorath civilian ships cross its space. Military ships should ask for permission first (and you have my permission to automatically have a Yamataian NPC grant permission for groups of NSN or LSDF up to 3 ships at a time. For larger groups, ask me). The only ships not allowed in Yamatai are spy ships like IPG ones (the IPG isn't allowed in Yamatai, period).
Freespacers ships can (and have been) allowed to cross Yamatai space. The latest news announcement by Yamatai also means that Yamataian forces aren't going to bother them by stopping them to ask questions. So if they want to run cargo across the YSE, that's not a problem. In fact, the Yamataian government's desire to placate the spacers is such that they're sometimes treated with extra niceness. The Star Army may offer them free water resupply, other handouts, or offer unusually high paying jobs to their hackers.
Poku Saeruo Degonjo ships of any type have unlimited travel in the YSE.
The Star Army of Yamatai is a highly competent, professional military and should always be shown that way. When a Star Army starship or other unit is shown in the RP, it should always be clear which ship or unit it is, using its name or registry number if available.