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If the pom files for your custom webapp are organized as shown in this example - you must change only one property. In the <properties> section of your parent pom change the version of the magnoliaBundleVersion property:

<properties>
  <magnoliaBundleVersion>5.7</magnoliaBundleVersion>
  <foobarModuleVersion>1.2</foobarModuleVersion>
  <javaVersion>1.8</javaVersion>
</properties>

Line 2: Set the magnoliaBundleVersion to your required version. That's all you must change on the pom files of your webapp.

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