mSource = systemcomposer.createModel('Source_Model_Allocation',true);
sourceComp = mSource.Architecture.addComponent('Source_Component');
mTarget = systemcomposer.createModel('Target_Model_Allocation',true);
targetComp = mTarget.Architecture.addComponent('Target_Component');

allocSet = systemcomposer.allocation.createAllocationSet('MyAllocation',...
     'Source_Model_Allocation','Target_Model_Allocation');

defaultScenario = allocSet.getScenario('Scenario 1');

allocation = defaultScenario.allocate(sourceComp,targetComp);

sourceComp2 = mSource.Architecture.addComponent('Source_Component_2');
targetComp2 = mTarget.Architecture.addComponent('Target_Component_2');

synchronizeChanges(allocSet)

allocation2 = defaultScenario.allocate(sourceComp2,targetComp2);

systemcomposer.allocation.editor

Simulink.BlockDiagram.arrangeSystem('Source_Model_Allocation')
Simulink.BlockDiagram.arrangeSystem('Target_Model_Allocation')

save(mSource)
save(mTarget)
save(allocSet)