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I'm working with a Windows Small Business Server 2003. I have very little server experience here and this one has some pretty specific issues with it I'm unsure how to address. The only source of information I have is exchanging emails with the owners kid who worked with it two or three years ago. His helpfulness is debatable, but he's also very busy and it takes 4-7 days to get a response to emails.

First off, this server has not been rebooted in months, maybe almost a year for what I can tell.. The guy said "The server is hilariously easy to break. The initial setup that was supposed to be run when the server was first installed was never done (as far as I can tell), so it will never complete."

The server is running Cyrious SMS, a piece of business software. I recently did a client install on another computer in this office, which will require me to restart this server - I'm pretty terrified to do anything big with this because if I break this I seriously have no idea what to do. Because of this I've been working very carefully and slowly with my decision making.

If I restart this thing, is everything going to go under? If not, how often should I restart it. I feel like I'm walking in a minefield whenever I touch this thing aha.

TheCleaner
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DIgou
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    Get a good backup – TheCleaner May 22 '13 at 21:17
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    Hire someone who knows what they're doing. Backups, backups, backups. Reboot monthly, after patch Tuesday; and after every major change (if for no other reason than to prove it will start on its own again). – Chris S May 22 '13 at 21:24

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This is a case where you REALLY need to hire an expert to help you get the environment straightened out. Your initial assessment is correct: you are walking in a minefield any time you touch this system.

A machine which has been left in a corner to accumulate neglect for an extended period is not the kind of challenge someone with very little server experience should be taking on - particularly if it does anything business-critical.
With enough years of experience you eventually develop a feel for this sort of broken, cruft-laden beast - a machine that has been without human companionship so long it's effectively gone feral, and will fight you before it lets you help it.

Now once you've hired your professional there are a few things you should make sure they do so they don't wind up breaking things on you.

For starters, like the commenters said, good backups are key.
If something goes wrong you want to be able to get back to at least some basic level of functionality.
The way you know you have good backups is by doing a successful restore test - so this might mean buying another machine to restore to and demonstrate that your backups will indeed WORK should the worst happen.

After that you can star to untangle the mess -- Given the fact that the machine is in an unknown state the way I would approach it is by building a replacement (on that shiny new hardware you used to prove your backups) and then migrating your data over to the new machine (using those backups).

Once you've built a suitable machine you only have to do the hard part -- maintain it going forward.
This means installing vendor patches in a timely manner, regular reboots like Chris S mentioned to ensure that you're never in a situation where you're afraid the machine won't come back if it gets rebooted, and investing the time to keep current on industry best practices.

Community
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voretaq7
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    +1 for new machine and migration. You can look into doing an SBS Swing migration (they even sell a kit). Get them updated, etc. – TheCleaner May 22 '13 at 21:44
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    @TheCleaner I didn't even notice that this was SBS -- I think Microsoft discontinued that, so a new machine and migration (to 2012 "Essentials" I believe?) is pretty much mandatory for ongoing support – voretaq7 May 22 '13 at 21:45