Yeah, there is a lot of jargon, although most tutorial sites I've seen try to not use too much. The problem is that one has to assume at least some things, or a single tutorial would have to be huge, including every possible explanation. This glossary may be helpful to you: http://www.swpearl.com/eng/scripts/dictionary/

A few things. I'm not sure which page you're referring to, but you don't have to install Qt the hard way. If you're not familiar with Package Management, read up on it on the UbuntuCat site. It's a system that allows for a modular OS and applications, central distribution and updates for everything, and also tracks all of your system files. Linux very closely follows the philosophy of "a place for everything, and everything in its place", and package management allows for that to work by tracking all installed files in a database. The standalone installer you downloaded is an example of the "last resort" option, because often such things leave untracked files floating around on your system, which kind of defeats the point of tracking them (all personal files should go in your home directory unless you have a reeeally good reason not to). That said, kudos for working out the permissions issue. The reason for that is simply security - when you download a file, it is by default not executable, so that downloading random e-mail attachments (in theory) isn't going trash your system without your say-so. Because most normal users are going to use only the package manager, it's not usually an issue, but I've seen newbies get hung up on that problem for a while. :P
Anyhow, to get to the point, if you want to use Qt on the VM OS (Ubuntu variant), then you install it with synaptic in the GUI, or apt-get in the shell. However, that won't install it into the actual SDK. When you run /scratchbox/login, it puts you into a special shell that can run ARM applications, and can be used for building and debugging. The "home directory" in that shell is actually located in /scratchbox/users/maemo/home/maemo , and you should be able to open a file manager to there and either drop files into it, or open files from it in a graphical editor if you wish. Note I say should - if it doesn't work, let me know. You may need to use the sbox shell to actually do the compiling, although I seem to remember hearing that it comes with a plugin for whatever IDE it ships with that allows to do it in the IDE... don't quote me on that. If you want to install Qt in the SDK environment, you have two choices: Qt 4.5 (stable, but not a full Maemo port, and not going to be supported by Nokia), which is in extras, and is called libqt4-dev (technically that's a lie, but it's split into modules, and that should install them all for you in a more simple way than otherwise), or Qt 4.6 (potentially unstable, but almost fully integrated, and will be supported soon), which is in extras-devel.
So yeah, to summarize the first bit: check the repositories for your program first, then look to see if there is a standalone installer or other less desirable method, and only then worry about compiling if you need to. Package management is great, but the problem is that most distros do it a bit differently from each other, so you can't just take, say, a program distributed by Fedora, and install it on Ubuntu. It's kind of a "blessing and curse" situation - if programs are available (and most big distros have many thousands of apps and libraries), they're (IMO) simpler to find and install than in Windows, but on the other side, at least with Windows any old download will work.