What you do is you actually treat systems as self contained files.
In the main .dat file for my Realistic space layout, you'll find the line:
planet data {
#INCLUDE rl_data_planets.sec
}
Which points to a file I have named rl_data_planets.sec.
This is a master map file, but look what's in it:
#ECHO * loading solar systems for First Contact...
#INCLUDE sf_data_planets_Sol.sec([r]=0.0,[a]=0)
#INCLUDE rl_data_planets_ACentauri.sec([r]=30.0,[a]=275)
#INCLUDE sf_data_planets_EEridani.sec([r]=82,[a]=85)
#INCLUDE sf_data_planets_TCeti.sec([r]=100.0,[a]=45)
#INCLUDE rl_data_planets_Sirius.sec([r]=65.0,[a]=135)
#INCLUDE sf_data_planets_W359.sec([r]=95.0,[a]=157.5)
#INCLUDE sf_data_planets_61C.sec([r]=90.0,[a]=0)
#INCLUDE sf_data_planets_R154.sec([r]=65.0,[a]=315.0)
#INCLUDE sf_data_planets_BSTAR.sec([r]=45.0,[a]=292.0)
#INCLUDE sf_data_planets_PCENT.sec([r]=40.0,[a]=270.0)
#INCLUDE sf_data_planets_Procyon.sec([r]=60.0,[a]=202.5)
You edit those individual systems in their own files and it will treat all the systems there as individually centered objects.
So the master file, here would say to then reffer to the file for SOL...
Here's SOL's actual file.
#ECHO loading Sol solar system at ([r],[a])
*
* class name rad angle mass ap bi temp hp sg ab tf
* --------------------------------------------------------------------------------------------------
Star Sol [r] [a] 1.0 30.0 Sun 5800 100 100.0 100 0
Planet Mercury 0.148 128.0 0.06 0.0 Mercury 800 0 .12 100 50
Planet Venus 0.165 * 0.81 7.6 Venus 600 0 .85 100 100
Planet Earth 0.2 * 1.0 1.0 Earth 300 70 1.0 100 100
Moon Luna 250 * 1.0 0.0 Luna 300 0 .15 100 100
Planet Mars 0.25 * 0.11 .10 Mars 260 0 .20 100 100
Moon Phobos 200 * 0.05 0.0 Aster1 260 0 .02 100 100
Moon Deimos 250 * 0.05 0.0 Aster2 260 0 .02 100 100
Minor Ceres 0.255 60.0 0.05 0.0 Aster3 180 0 .02 100 50
Minor Pallas 0.257 177.0 0.05 0.0 Aster4 180 0 .02 100 50
Minor Juno 0.26 263.0 0.05 0.0 Aster1 180 0 .02 100 50
Minor Vesta 0.262 273.5 0.05 0.0 Aster2 180 0 .02 100 50
Minor Astraea 0.265 186.0 0.05 0.0 Aster3 180 0 .02 100 50
Minor Hebe 0.267 61.5 0.05 0.0 Aster4 180 0 .02 100 50
Minor Iris 0.27 269.0 0.05 0.0 Aster1 180 0 .02 100 50
Minor Chiron 0.272 73.0 0.05 0.0 Aster2 180 0 .02 100 50
Minor Hermes 0.275 180.5 0.05 0.0 Aster3 180 0 .02 100 50
Minor Icharus 0.28 59.5 0.05 0.0 Aster4 180 0 .02 100 50
Minor Eros 0.285 80.0 0.05 0.0 Aster1 180 0 .02 100 50
Minor Achilles 0.29 174.0 0.05 0.0 Aster2 180 0 .02 100 50
Minor Apollo 0.275 280.5 0.05 0.0 Aster3 180 0 .02 100 50
Minor Amor 0.275 57.5 0.05 0.0 Aster4 180 0 .02 100 50
Planet Jupiter 0.3 * 318 90.0 Jupiter 160 100 20.0 100 0
Moon Callisto 525 * 1.47 0.0 Callisto 160 0 .21 100 100
Moon Europa 475 * 0.65 0.0 Europa 160 0 .08 100 100
Moon Ganymede 425 * 2.01 0.0 Ganymede 160 0 .24 100 100
Moon Io 375 * 1.21 0.0 Io 160 0 .11 100 100
Planet Saturn 0.35 * 95.2 30.0 Saturn 130 100 2.1 100 0
Moon Titan 400 * 1.84 0.6 Titan 170 0 .30 100 100
Moon Rhea 350 * 1.0 0.0 Rhea 130 0 .10 100 30
Planet Uranus 0.4 * 14.5 10.0 Uranus 110 100 1.20 100 0
Planet Neptune 0.45 * 17.1 9.0 Neptune 100 100 1.15 100 0
Moon Triton 300 * 1.84 0.0 Triton 100 0 .08 100 10
Planet Pluto 0.46 320 .002 0.0 Pluto 60 0 .03 100 100
So what would load here is the Sol system, and it would be loaded in the Distance 0, Angle 0 as specified by rl_data_planets.sec. (Specified by r= and a=) All objects in the SOL file would be positioned reletive to SOL.
It then loads Alpha Centauri at position Range, 30.0 , Angle 275 degrees... everything under alpha centauri's file would load based position 30, 275. With 30, 275 being treated as zero.
This would continue on down the list. Essentially, the map builds into a kind of self nested setup.
I hope that helps.
EDIT:
So to duplicate the Tholean system with seven suns... really make one system. Place the planet you want in it... and then make a bunch of individual systems with one 'sun' in them and use some trig to figure out how to position them. (You're going to need trig for anything other than a center position when you're trying to center those stars on the tholean planet without using the planet as the actual refference point.)