So doesn't aperture make the image library as a disk image (or something like that)? I was under the impression that you can only import a master folder and have to organise images internally meaning that to view folders you have to open aperture as they aren't visible in the Finder.
Aperture is extremely flexible: you have three choices -- and you can change your mind at any point!
(1) You let Aperture manage the library. Pictures you import get copied into your Aperture library which is just a bundle. You have full access to all of your files in the Finder: right-click the bundle and select Show Content.
(2) Aperture can deal with `referenced' images: upon import, it only links to wherever you've decided to put the images. This means, you're in charge and responsible for managing your original image files. Just like Lightroom, the Aperture library only contains metadata, versions and previews.
(3) You can mix and match the two modes, managed and referenced, on a
per-photo basis. You can, for instance, reference whole projects. That's useful if you want to move finished, old projects onto an external harddrive.
There is probably a lot of debate on this already but does Aperture have a better or worse rendering/colour engine than Lightroom? Can I expect Aperture to have better colour reproduction or is their a standard across all photo editing programs?
There's no real answer to that: what is a `better' RAW converter depends on individual taste. Many people would claim that your camera's manufacturer's RAW converter yields the best result. Unfortunately, these don't integrate with Aperture or Lightroom. And they are usually a pain to use. That's why some people use Aperture or Lightroom to sort their pics and their picks get individual therapy in the RAW converter of choice.
What about when you go from Aperture to Photoshop? Do the colours alter as you are using different program manufactuers, I guess that is more to do with colour space though really.
No, the colors don't alter as Aperture renders the file into a tiff or psd (depending on your preferences). Hence, they are rendered exactly as they are in Aperture.