First thing to do is read the INSTALL & README files for instructions on compiling the code. Generally, you'd do the make in the top directory of the source tree. As far as appling the patches goes, use patch, something like:
patch -Np1 < nameof.patch
Patching is also generally done in the top directory. Which one to apply? Open the patch file in a editor and see what it does, else read any README that comes with, decide based on that.