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I've setup OS X Server 5.1.5 on El Capitan 10.11.5. I've enabled the caching server, open directory and profile manager in OSX Server.

I have iOS and OSX devices enrolled, and the configuration payloads are working well with my devices/device groups.

Although I can get the configurations to work, I can't figure out how to manage app or OS versions.. Is it possible to remotely force upgrades of the OS from OS X Server/Profile Manager? I have a number of MacBook Air's on Yosemite, and would like to force them all to update to El Capitan.

Jeremy
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You'll need to use ssh or 'Remote Desktop' from Apple to apply these updates to the clients. A pre-requistite for this, that you may want to go around and setup on all your OSX clients once, anyway, is that in the Sharing preferences, ssh aka in OSX gui-land "remote management," and possibly also "screen-sharing" is enabled.

The installations on your OSX clients will fall back on the settings in System Preferences -> App Store (if needed see the imagenear the bottom of this answer), and if all of the options were "checked," the clients would have probably already upgraded themselves to El Capitain. As far as I know these updates, if not explicitly allowed, are applied only on an admin login, or on a restart (e.g. a scheduled restart from Energy Settings -> Advanced).

So assuming that you have the settings in System Preferences set to (not) allow automatic updates, or to only allow security updates, how I frequently use them on my clients, there will not be any other semi-automated option.

Apple does offer an Application called Remote Desktop, which provides a bit more tools; it is really fun, but to be honest, I've used a lot of time trying to use it, or find ways to look like more of a rock star by doing command-line installations in OSX, but in many of my use-cases, the software requires some type of dialogues that can't be scripted out or included as an argument to installer or pkginstall.

The closest feature I know of from the official Apple tools so-to-speak, is to use Remote Desktop or another application where you can do ssh into multiple systems at once (e.g. Puppet) and then 

sudo softwareupdate -i 'OS X El Capitan Update-10.11.1'

or apply the exact update that you wish to use

you can first use softwareupdate -l (--list) to see which update it is that you would like to apply

OSX preferences system app store updates choices 2013

If you don't have as much OSX experience as I've assumed, we can expand the answer or comment back and forth until we've got you covered.

It should work well for you to use Bash, as described above, since you are looking into the one, specific udpate, after you find out what it's specific name is. I've called it "OS X El Capitan Update-10.11.1" above.

bourneN5years
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    Thanks for the great info. It's unfortunate and kind of surprising that Apple provides no way at all to update many macs at one time.. I will look into Puppet.. – Jeremy Jun 20 '16 at 17:17
  • This might be a completely separate question now.. but I tried to update using the softwareupdate tool. When I ssh into the remote mac and run "softwareupdate -l", it lists 3 updates (Yosemite Recovery, OSXUpdCombo and iTunes). However, when I look on the AppStore of the actual machine, it lists completely different updates: GarageBand, KeyNote, Pages, El Capitan, etc.. Any idea why? – Jeremy Jun 20 '16 at 18:18
  • You could definitely add that as a separate, specific question, like (only for example) "What is the difference of the App Store and softwareupdate on OSX," but in this case at least as far as I can tell, it is very related to the Answer, so be sure to link it here. I will get back on it. – bourneN5years Jun 21 '16 at 08:30
  • Re: Puppet; it is not always simple, or even possible, to use standard UNIX or Linux (or more generally, FOSS applications) on OSX, but one huge plus is that on **Server Fault** and the other forums, you'll have an army of people here to help that are awesome with those tools; whereas OSX server alone, or the Server.app are (generally) used by specific groups, for example media firms or studios, or by really experienced people as additional tools for their Macs. – bourneN5years Jun 21 '16 at 08:33