Already found the answer in the documentation. I can use the Stop Service function.

Our previous installation is developed with InstallShield 11. A few figures:

IS11 InstallScript Setup: 45,400 KB (package size)
Patch (Differential Release) from Version 1.20 to 1.30: 9,403 KB (patch size)

And now the same with SetupBuilder 5:

SB5 SetupScript Setup: 37,304 KB (package size)
Patch from Version 1.20 to 1.30: 1,345 KB (patch size)

I am impressed! Just noticed the footprint is only 120 KB and the engine is fully scriptable! First I thought the patch process failed - in a blink of an eye the SetupBuilder installer told me "Patch successfully applied". Took only a few (5 or 6) seconds. The same process with InstallShield took 55 seconds.

Thanks for a great software product.