This is how you do it:

Do the absolute least that you possibly can. If that doesn't quite solve your problem, do a little more.

Perhaps you've missed the point of programming in Perl - easy things are easy, hard things are possible. If you want a system that's going to hold your hand through every conceivable little thing and think for you - then switch to C# and use Visual Studio. Everything just clicks together right out of the box and you don't have to think. Of course .Net + Visual Studio has its own problems (being from Microsoft and only runs on Windows being the root of them).

There is no ONE TRUE WAY to do anything. You have to adapt to the situation at hand.

If you are worried about doing things too difficult for others to understand, then try doing what everyone else does:

• Use Git/SVN/CVS/whatever. Don't use something you invented.
• Use normal folder structures (~/projects/someproject/lib etc t sbin whatever) is fine.
• Perl has this great module installer thingy called "CPAN" - you may have heard of it. Don't install modules in your application's directory, as they may be out of date.
• Use the simplest thing that could possibly work! Every additional requirement is just another flaming hoop you jump through. No hoops = no jumping.
• Look at Padre - it's a large project and has many dependencies. It also installs quite nicely. Look at the project structure - it has many developers and everyone seems to get along just fine working together. It is a success - do what they are doing!