Vague list of steps but effective. I am running a personal server also and here is how I update it.
1) get the latest source (git pull)
2) compile
3) copy into appropriate directories like you did when you first built it
4) get latest db (record the file date somewhere, you will need it)
5) source drop_system.sql
6) source latest peqdb sql
7) source required sqls from last date you updated (thats why you record date)
7) source any custom sqls (i have two, custom_loot.sql and custom_rules.sql)
start playing
Only issues I ever have are when the source is buggy but that is not often. Also I only update when I see a change in the change log that makes a dfference for what I am playing. For example, the latest source as of this post includes some rogue changes so if I were a rouge then I would update.
Also a good idea to copy your current server files to a flash drive since you know they work in case something goes wrong with the update. Dont copy the maps or quests, just the binaries should do.