I've Cloned my Hardrive.. Will I lose my apps?

You shouldn't. Try booting from your external drive to be sure.

 

If you've cloned the hard drive (not just backed up the Applications folder) then you won't need to reinstall anything.

 

Is Carbon Copy different from Time Machine?

 

I found that the clone I made with carbon copy slower than the original drive, I think because all files were copied in alphabetical order, yet during a traditional install the files would be in a more logical order, for an operating system. I think if I did it again I would use carbon copy clone as a backup but try and migrate using my Time Capsule.

 

Carbon Copy can work like Time Machine, but its main purpose is to create a clone of your hard drive.

 

What is the best way to sync two macs so the files are constantly kept the same on both machines?

 

you can use time machine... if you're still with 10.4... you can use Carbon Copy Cloner to do a full backup... then set it to do an incremental backup and it will copy excatly what you have on your computer or put the changed files in an archive... so its like time machine. you have the changed files in there so its no problem... the thing is over time, it will take up more space in your hard drive.