Only the Navy Headquarters can be identified by their call signs.
This is not the case for all other stations; the HQs do communicate with a multitude of stations which are on ships or are land based stations for supplies, logistics, training or for coastal defense.
We are monitoring Morse networks, which to a great part are for training of operators. Since many years the same call signs are used, but that doesn't necessarely mean they are used on the same station. I do not think the Navy has any interest to reveal their structure - not even for training networks. Long-time monitoring of the same frequencies proves, that one operator handles more than one call sign; this becomes obvious, when his keying is easely recognised and when he mixes up call signs.
Only Radio Direction Finding with professional equipment can bring us further. Experiments with a Crossed-Loop RDF and Magnetic Loop Antennas have started, but there is still a long way to go. More about my RDF here: Radio Direction Finding .

A spreadsheet with CIS Navy callsigns/traffic of the past year can be downloaded here: Downloads
If you know more about the allocation of Navy callsigns please let me know.

The Navy callsigns have the following formats (L = letter, F = figure):

Special Purpose Call Signs

There is a series of call signs which are used for a certain purpose or by certain stations.

Naval Air Transport
Aircrafts always use 5-figure call signs, which are not re-used. An aircraft or a route cannot be identified by the call sign. More here: Naval Air Transport Units .

Collective call signs
Certain collective call signs do not stand for a fleet or a task force, but for an area.
Navigational/Gale Warnings to RGX94 always concern French Waters, such to RBE86 concern the Ionian Sea and Tunesia and the Syrte and such to RIP90 concern Turkish Waters and Aegeis. Weather Forecasts to RKZ probably include the Mediterranean Sea.
It is not yet clear if this is valid for REO, RLO, etc

The RJxxx Series call signs
There is a series of call signs, which do not answer on the primary frequencies 8345 and 12464 kHz and they can be found in Simplex mode on a frequency out of a pool; the busiest being 8120, 8128, 10796 and 13469 kHz.
The following, and for sure many more, are concerned:
RJC66
RJD25, RJD35, RJD36, RJD38, RJD46, RJD52, RJD69, RJD71, RJD77, RJD80, RJD85, RJD87, RJD99
RJE56, RJE58, RJE65, RJE67
RJF48, RJF95, RJF96
RJH25, RJH41, RJH57, RJH63, RJH69, RJH77, RJH90.

RJE56 always is the NCS, some observations make me believe, that RJE56 is operated by Moscow HQ.

RJH45, RJD38, RJF41, RJE73, RJH74
These call signs might be operated by the Navy's oceanographic service.
They receive messages of the following format:
From RJQ84 to RIT: QTC 224 21 23 1634 224 = for RJH45 RJH74 = 23121 .....(5FG with many slashes and zeros).
The first txt gr starts with the day of the month and follows, what looks like a Bathythermal Report (temperature profile and salinity of the Sea). RIT will pass on the measured results to RJH45 and RJH74. These are not weather data, the first group will then be "jjxx" or "kkxx" in the Navy format.