Sounds like you have come a pretty long way! It's not easy to get started with Linux, and once you have managed to overcome a few big problems it usually gets a bit easier, simply because you start to know the drill and feel at least a little bit comfortable.
Doing things over and over again until you get them right is often a good thing. It is also the best way of actually learning, so don't worry about that. It took me quite some time to get comfy with adding Linux to the NT bootloader in dual boot systems, but by now I could do it in my sleep. That's practice.
As I usually do it:
1. Update kernel and install it (if that's what I want to do)
2. Update /etc/lilo.conf and rerun /sbin/lilo
3. Copy the boot block to the Windows partition or to a floppy: dd if=/dev/hda5 count=1 bs=512 of=/mnt/floppy/bootsect.lnx
(if /dev/hda5 is the Linux root partition and /mnt/floppy is where the floppy is mounted)
As for keeping my system clean - I always keep a directory called ~/build where I unpack and build software so I don't litter my home directory or have sources spread out all over my disks. Software that you install from source often have an "uninstall" target in the Makefile that allows you to type make uninstall
as root, so keeping the sources can be a good idea.