I'm not sure you'll be able to work around that with your current setup.
You see, with Ubuntu 11.04, they went with their own variant of the global menu. Some love it, some hate it. I personally don't prefer it. The global menu as of now I don't know how to edit. That's why your min/max/close buttons go to the top left because that is their home location in the global menu. If there is a way to edit that, I personally don't know it. The default interface is known as Unity, and Unity is in its infancy stage now so customization of it is extremely limited. Future releases may give you the ability to customize it the way you like, but right now I'm not sure it's possible with that *exact* setup.
If you run another desktop environment, such as Gnome 3.0 "Shell" or XFCE, you will have full capability in making the changes you want. In fact, in XFCE (which resembles Gnome 2.X where you had a panel at the top and a panel at the bottom) you can change it right within their window manager control panel.
I'm not sure what your experience is with Linux, but something you'll have to get used to is the vast amount of choice you have. No other platform has the amount of choices we Linux users do. If you don't like Ubuntu Unity, you can choose IceWM, Gnome Shell, XFCE, LXDE, KDE, OpenBox, and the list goes on and on... So while you may still be on Ubuntu, you have a totally different interface running on the fore-front depending upon which desktop environment you install. So basically, what you are trying to do *currently* (I say currently because it may change in the future) isn't possible with Ubuntu Unity, other desktop environments built on top of Ubuntu may. Personally, XFCE may be the safest route. Gnome 3.0 "Shell" is done via PPA and really changes a lot of system variables since Ubuntu 11.04 is still Gnome 2.X based. 11.10 will bring native 3.0 support so it should be a lot less painless. This is all assuming you are sticking with Ubuntu. After all, Fedora 15 has native Gnome 3.0 Shell support right now, and it works well. But Fedora isn't exactly my cup of tea.
Sorry I couldn't give you an exact answer on your question, but there are choices and alternatives if you want to venture out that way. Let me just iterate a very important step prior to doing massive system changes. Backup Backup Backup Backup Backup Backup.
If you have any further questions, by all means.