For #1
All I meant to say is that if when you make backups (and you should always make it a habit to maintain good backups because every hard drive will eventually fail.) MANY people look at a hard drive they bought to make their backups and think "Gosh there's a lot of extra disk space on there... I could be using that to store more of my stuff." But if you keep your working data AND your backup data on the hard drive, then when the hard drive eventually fails, you'll have lost everything (both the working files and the backups). That's why I emphasize keeping backups and working data on separate disks.
For #2
A disk drive stores files in little "chunks" on the disk called "blocks". Little files can usually fit into just a single "block", but big files can require several of these "blocks". If you need to save a big file, (and lets say it needs 10 "blocks") the Mac will try to find a spot on the disk drive where all 10 of those blocks are all near each other. In doing so, when it goes to open the file, all of the data is essentially in one convenient place so it can read all of the data quite quickly.
If the disk is nearly full then there wont be a nice convenient space for a large file (e.g. you wont have 10 blocks in a row which are not being used.) This will force the Mac to tuck data wherever it can and that means the disk drive might have to go to 10 different locations to read just one file.
This slows down your computer... not just for Aperture... for everything. By making sure you have a fair amount of free space on the disk drive (at least 10% of the disk space should be free, but the more free space you can give it the better off you'll be.) you'll keep your computer running faster.
For #3
Perfect! I have several friends with Macs (most of them run iPhoto). The trash in iPhoto works the same as it does in Aperture. I was surprised (I probably should not have been) that they had never noticed that iPhoto actually has it's own "Trash" can. They assumed that if they emptied the "Trash" on the Mac's dock, then they had freed up the space.
For #4
This is the most complicated. RAW does take much more space than JPEG.
But the main point here is that the Aperture library uses two different kinds of data to load and render an image. (1) it uses the original 'master' image (sort of like the 'negative' that comes out of a film camera... this image is never directly edited or manipulated in any way.) and (2) it maintains a list of every adjustment you've made to that image. BUT... #2 is just a list (the adjustments are not stored as images).
When you view an image in Aperture in which you've already made many adjustments, Aperture does two key things. First it opens the "master" image and displays it, and second it reads through the list of the "adjustments" you've made and it re-creates those adjustments on-the-fly. When it finishes processing the list of adjustments you will see an image that looks just like it was when you last left it.
In contrast, iPhoto does not maintain a list of all of the adjustments you've made. iPhoto actually edits the image as you adjust it and it re-saves a new copy of the image with all of those changes. So if you were to later decide that you liked all of your changes except one, and wanted to undo that one change, you cannot do that with iPhoto (you can "undo" the last thing you did as long as you haven't saved.) Aperture is completely different. In Aperture if you don't like just one of your changes, you can selectively turn off that change (or just change it to something you like better) without affecting any OTHER change. This is much more powerful.
Since the "master" image data can be large (especially if it's RAW) and the "adjustment" data is just a list (e.g. text data and uses hardly any space at all.), and since Aperture is used by professionals... many of whom shoot a LOT of images in a day/week/month/year, Apple makes it possible to separate where you store the "master" images vs. where it stores "everything else" (the adjustment data as well as all the other data that Aperture manages for you.)
If you store the original "masters" somewhere else, Aperture calls these "referenced" masters. If you import your masters into the Aperture library then Aperture calls them "managed" masters.
In a sense, "referenced" masters is a somewhat advanced concept. I have some ground rules for using "referenced" masters. Before using them you should (a) understand how they work, (b) have a good reason to use "referenced" masters (other than "well it sounds like a good idea") (c) have good organizational skills (Aperture wont organize "referenced" masters for you... that's up to you. So you should probably have a good scheme for keeping track of everything.) (d) you should not attempt to directly manipulate any image once it becomes a "master" and is used by Aperture.
Still confused about "referenced" masters?
If so, then just select the option that says "Store files: In the Aperture Library" when you do an import and you wont need to worry about any of this. Aperture will manage everything for you (it is quite good at it) and the only thing you'll need to do is make sure you don't run out of disk space.