Dynamics CRM Noob

I'm CRM newbie but a long-time .NET and SharePoint developer. I'm using CRM Online and having lots of problems getting oriented to customizing solutions. Here's what I need to do:

1. I have a free managed solution from Microsoft that I need to install in CRM online, then customize.
2. I tried installing this managed solution using the PackageDeployment.exe tool. It installed fine. But when I did the customizations they seemed to take place at the Systems Solution level.
3. I would like to create a set of unmanaged customizations to the managed solution that I can install on top of the managed solution. Is that even possible?
4. What steps do I need to take to: (a) Install the managed solution; (b) Create customizations to the managed solution that exist independently as a set of unmanaged customizations; and, (c) Export those unmanaged customizations as an unmanaged solution (I think I'm using the correct terminology here).
5. I would like end up with a situation where I can install for my customer: (a) The freebie Microsoft solution and (b) On top of that my customizations to that freebie solution, so the end result is a CRM solution that I design.

I hope I am clear.

Thank you very much in advance for any help.

Clyde