How do i transfer an app and its contents to new mac

Hi,
I've just got a new Macbook with Mountain Lion. I backed up my old Mac (Lion) using Carbon Copy Cloner - although i'm not sure whether it was a bootable back up (when i plug the external harddrive in it shows multipe folders - users, systems, library, applications etc...).
How do I transfer Aperture , Final Cut Pro, iWork, and iLife and all of their saved contents (projects, pictures etc...) over to my new mac. The Genius today told me that because I didn't do a time machine back up I should be careful when transfering these as certain program files may have changed and will have an affect on the new machine...
Also, I should mention that I don't have Final Cut Pro, Aperture or iWork installed on my new mac.
Any help would be greatly appreciated...
Thanks, Aaron

Okay cool.
But if the carbon copy was made on Lion and my new OS is Mountain Lion, will this have an affect on the way apps work??
The only apps i'm worried about are iWorks (as I dont have original disk so need to transfer these apps via carbon copy), as well as iPhoto - as I have all my photos on it.
Should I just transfer the iWork apps via drag and drop (then do any updates they say I need. and then when I drag and drop the iWork files (pages files mainly) will they work fine?
And with the iPhoto photos, should I just drag and drop the iPhoto library file - as I won't need the App as it's already installed on my new mac...
Just a little confused as to how my new mac will accept the Apps and it's files as they are from an older OS...
Sorry if this is a little confusing...
thanks so much.....

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