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generally, you don't need to recompile your kernel unless you're having hardware problems. most distros come with the default kernel pretty well shock-proofed.
as for ./configure, it mainly searches for dependencies and locates them for the compiler. if you've looked through your file system, then you've probably noticed your /usr/bin/ and your /usr/local/bin directories. these are the most common places for packages and programs to be installed, and a very large part of the ./configure script goes to finding out which directory you have your dependencies installed in. that's one particular part of any *nix that tends to vary, and the configure script makes it relatively easy to find what the compiler needs where. the compiler also requires a few flags, and the configure script sorts those out too. it writes all that out to the makefile, and gets it ready for compiling, so you don't have to memorize compiler flags and directory dependency allocations, ect., ect...
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