Whats the difference between applications that come in the form of binarys and applications that come in the form of source code. And is there going to be a difference in the way they are compiled, same commands etc. Usually the work great, but are only suitable for certain configurations. This is not all that common if you stick with what comes with your Linux distribution, but if you start customizing your system, upgrading here and there, you may put yourself in a situation where some of the precompiled binaries won't work anymore. Most binaries that are packaged properly will check for all the required files at installation, but you don't have any guarantees.
Source code is the raw code.
You have to compile it yourself to create the binary. This is slower and a little more difficult than installing a binary, but its not too troublesome once you get the hang of it. You can still upgrade yourself to a state of broken-ness, but you can usually recompile the code to fix some of your problems. There are a few other pro's and con's of each method, but the general idea is that the Source is RAW and the Binary is more or less ready to install. I have found several instances where the only way I could get an application to work on my system was to compile my own source code.