Rockbox Utility uses sansapatcher directly, so there shouldn't be any risk in using it. An updated version of Rockbox Utility was just released (m1.0.1, to be exact

) which includes various bugfixes that got reported with the first release. A lot of testing is still needed, so trying it (and reporting your result or found issues) is more than welcome ...
You need to set the e200 to MSC mode first as the manual describes. There is no change in this step by the use of Rockbox Utility.