There are 2 ways of using them.
1) The manual, tedious way, which I will not go in depth.
2) The easy, mod selector way.
1) Basically you need to use rabcdasm to decompile the client, look in the .xml file to know which parts of the code need to be inserted where.
For example when you see this:
Code:
<code file2mod="com/company/assembleegameclient/objects/GameObject.class.asasm"
line="1808">
noDebuffs.txt
It is telling you that in the line 1808 of the GameObject class which is located inside of com\company\assembleegameclient\objects you need to insert the content of noDebuff.txt
Once you've inserted all the pieces of code you need to recompile the client.
The reason I won't go in depth with this method is that mod selector does this automatically.
2)To use the sources with mod selector you first need to create .zip's for the mod selector to interpret. The old .zip's that are inside of the \mods folder will not work, but you can update those. For example, unzip 8.0.0_noDebuffs.zip. You'll see two files have popped up. One is 8.0.0_noDebuffs.xml and the other one noDebuffs.txt. In this case you only need to change 8.0.0_noDebuffs.xml So what you do is open it with your prefered text editor (Notepad++ recommended) and update what needs to be updated. In the case of noDebuffs, you only need to update the lines. Once you've done this you rezip it (don't forget to delete or at least move the older hack) . In some cases you'll need to update much more than just the lines.
Either way, source codes are irrelevant once a proper mod selector is released since all the new source codes are the ones being used in the updated \mods folder, which makes it unnecessary to touch anything.