To answer my own question:
The function [ModelNew,g,T,Ti]=balreal(modelOld) gives a new model which has as many states as the old model BUT they are in decending order of importance. It also gives g which shows how important each state is and T which transforms the old model into the new WHICH CAN ALSO BE USED TO TRANSFORM THE INITIAL CONDITIONS, Ti is the reverse transform
newIntialConditions=T*OldIntialConditions;
modred can then be used to reduce the model order to whatever you want
ReducedModel=modred(BallencedModel,ReduceStatesTo:NumberOfStatesInOldModel);
The initial conditions must of course also be trimmed to the right number of states