We are developing an auto updater script in house, however, until this tool is available, the upgrade process must be done via uninstall & reinstall. Customization can be categorized as follows
1. Template & UI customization: please use the template overwrite feature of Joomla 1.5
2. Code/form customization: You should make a list of steps by steps which file you change & how you does the change. Eg
<blockquote>Change #8: Change joblist view
In file com_jajobboard/list.php, search for
++++++++++++
xxxx
++++++++++++
Replaced with
++++++++++++
yyyyy
++++++++++++</blockquote>
3. Admin configuration/Forms/Custom fields
As when uninstall, your database of job board will not be affected, so what you have done to your DB will be the same. When reinstall, the component may insert or modify some database structure but most of them will be safe.
Anyways, the very first thing you MUST do before upgrading is making a full back up of files & database
