If you have an accumulation of software updates to install but don’t want to be interrupted—say that you’re working with some of the apps that need updating, or you need to install a system update that requires a restart—you can have OS X bug you about it later.
Pop open the App Store app if it isn’t already, then go to the Updates screen (selecting App Store… from the Apple menu will take you there as well if you have any updates waiting to be installed). Next, look for the Update All button toward the top of the window, and click the segment of the button with the downward-pointing triangle. A menu will pop up that lets you choose whether you want to install updates now, or have OS X try again in an hour, try again tonight, or try again tomorrow.
Choose whichever option you want from the menu: If you told OS X to try again later, it will remind you at a later time that you have updates that need to be installed. I like to download updates overnight since it’s the least disruptive, so with that in mind, I’d suggest selecting Try Tonight.
If you have any other user accounts logged in on your system, you’ll need to log out of them at some point before OS X tries to install updates, so be sure to do that.