Resist the urge to bend Maven to your will. Even though you can redefine where things are located, not all plugins will recognize the new locations. Besides, one of the perks of Maven is that every project looks the same and is built the same way. Well, at least until you get into very complex projects that invoke a lot of specialty plugins, but even then you can define project types and every project of that type can look the same. My recommendation is to reformat the project, possibly breaking it up into multiple projects, to fit the Maven best practices. I spent the last half of last year doing this for a dozen projects, which turned into about 20 projects by the time I got done. But everyone is happier with the results than what we they before (it was pretty much managed chaos).
If you are still set on breaking Maven, you will have to pay close attention to the properties available for every plugin goal. You will also have to know the pom.xml structure inside and out. Between the pom.xml settings and the plugin properties,
you should be able to relocate almost anything. I highly recommend that you do not attempt this until you are very familiar with how Maven works and have spent some time building things the maven way. If you are new to Maven, don't even think about trying it.