I haven't found anywhere anything like the Fleet write-ups on where the administrative boundaries are, who is in charge, when the leaders are appointed or removed.
Mainly because the IISS has never been "defined" down to that level of granularity. The impression that most IISS published materials in CT convey is that of a sort of decentralized amorphous "blob" of a service that just "does stuff" on the regular. In that respect, the IISS is less "chain of command" structured (like the navy) and more just "administered" by local authorities in the bureaucracy providing the funding for operations.
On a somewhat practical level, the scope of the IISS is simply "too large" for any one person to be in charge of it all. There can be a centralized policy making body (probably back at Core) that disseminates out directives to the various offices of the service, but a lot of the day-to-day decision making is going to be more local.
My personal theory of how the IISS is organized is that there are "layers of HQs" at the subsector, sector, domain and entire imperium levels ... but the "farther away" those HQs get the less "relevant" they become to those day-to-day operational experience of individual Scouts (mainly due to communication lag times). The sheer scale of the Third Imperium means that any directives decided upon back at Core can take YEARS to be disseminated out and implemented out towards the fringes, such as the Spinward Marches or the Solomani Rim. That kind of comm lag means that anything that needs to be dealt with in relative real time terms can rarely afford to be sent too high up the food chain (even with regular XBoat services for communications). It simply takes too long for a lot of things to have decisions "kicked upstairs" ... meaning that bureaucratically speaking, saying that something is "above my paygrade" and needs to go to a higher authority is a great way to delay (and hopefully bury) any inquiries along those lines.
So if you're in the Regina subsector, but your request for
{insert something here} needs to be forwarded on to the command staff at
Katarulu/Trin's Veil (not
Efate/Regina) for a decision/authorization is one way to bureaucratically tell someone "shut up and go away" so they have to get out of your face/office.
Has there been a write up at any point?
Not really ... which is largely a good thing.
By not "defining" the IISS too hard, it becomes malleable enough to be whatever Referees need it to be for their campaign settings.
Who is the IGS leader for the Rigina Subsector?
To my knowledge, never specified.
That then leaves sufficient room for Referees to make up whatever they need for the purposes of their campaign should that information become relevant to their setting.
When your paycheck comes back a Cr0.06 for the month, to whom to you complain?
Nearest scout base will have admin staff who can resolve payroll issues.
How does your paycheck arrive at all?
Electronic direct deposit into your personal bank account, the balance of which can be withdrawn from at most starports (D+ I think?).
Who has authority to authorize a cultural survey?
Scout base admin staff ... assuming the base has unclaimed funds sufficient to finance the survey expedition.
What probably happens is that whenever a base gets a fresh injection of operating funds for the base, there will be a bidding process for missions in need of funding that will be evaluated by the base's admin staff for approval. Sort of a RFP (Request For Proposals) type of thing. Each base will get its own budget of funds for such priorities ... meaning that if you get turned down by the staff at base A, you could take your proposal to the staff at base B and perhaps be approved. In that case, base A simply had other (read: higher) priorities for their funds already in the pipeline, rather than being the case that your request had no merit and thus would not be funded by ANY scout base anywhere. Nuisance requests will probably wind up getting you blackballed everywhere at every base (GO AWAY!), but legitimate requests can simply keep trying to compete for authorization, shopping around the proposal at different bases or over subsequent fiscal cycles.
Who can request that a planet is isolated for its own safety?
That is something that is probably "kicked upstairs" for finalization.
The subsector command can probably impose a temporary quarantine (pending longer term approval at higher levels).
Sector command could make it permanent (until overturned) upon review.
Domain command would be the point of appeal to get the designation overturned.
That's the way that I would handle it, anyway.
Isolating a planet for its own safety is something that needs to happen rapidly, so "closer" elements of the service need to have at least temporary authorization power, since time could be a factor in a rapidly evolving situation.
Who do those research stations report to?
Do you have clearance for that information?
No?
Then you don't need to know the answer to that question, do you?
As a matter of practicality,
Imperial Research Stations don't necessarily report to the IISS specifically. They could, but they could also be civilian/paramilitary/military research installations, meaning there's a pretty wide range of potential "clients" for reports from those stations to be sent to. Definitely NOT a one size fits all kind of deal.
Where is the external mapping group based?
EXTERNAL mapping would presumably be based around the fringes of Imperial controlled space (think of the Five Sisters subsector in the Spinward Marches context as home base for explorations into Foreven Sector).