I'm not familiar with SiteKeeper, so I jumped out to their page to do a little research. SiteKeepers offers two modules (both sold separately): inventory and software distribution. If this is all that you need in your organization, it sounds like a good solution.
On the other hand, SMS includes (all contained within the product, you don't have to pay extra for additional modules) inventory, software distribution, reports, queries, SQL server support, remote management tools, software metering, smart distribution technologies (very kind to distribution over slow links and checkpoint restart), and full patch management (includes automatically downloading patches from Microsoft, creating distribution packages, and vulnerability reporting).
With SiteKeeper you are paying roughly $34 per each computer you install the client piece on (that's for both modules). For SMS you pay considerably less than that per client, with all "modules" included in the price.
If you're already stuck with supporting SiteKeeper, you may want to contact the vendor and ask to speak with current customers for help. I really don't hear of anyone using the product, and I participate in the systems management community daily.