Hi!
Since I'm familiar with FieldPoint PACs, I'll refer to that (but maybe it is similar for cRIO...).
An embedded application (standalone), runs entirely and independently on the PAC, while if you're not doing this, you'll have your computer, with LabView, which is controlling the PAC. In this mode, application is dowloaded in PAC's RAM, so when you reboot controller, application will be lost. If you build an embedded application, you can provide for application to boot authomatically at boot, each time the PAC reboots. These are some basic stuffs on embedded applications with LV.
To deploy an application to a PAC, you need LabVIEW + Real-Time module. Without it, you can't build an embedded application on PACs.
usually, the file dowloaded is an .exe, and some libraries. What would you like to have, exactly? For example, I think you can buy a simple .exe, which is universal, which loads VIs dinamically, so you can download directly VIs, but I've never tried this way....
Deployment license, I think, refer to PCs, id est, when you use a PC or PXI as embedded target, in PACs, you have it bundled (it seems to me) whit the PAC you buy, so you don't have to buy an extra license for every PAC you ship with your application. Otherwise, if you develop a Real-Time application for a PC, you will ship PC + OS licensed + Real-Time extension licensed, but this is not your case, since you'll use PACs.
The maintain problem... I've already faced with! Simply, for my needs it was enough to make an application which loads configuration files, depending on different task the controller has to do. If you have to dowload a completely new version of VI.... it's better to deploy new application from LV. But maybe you can bypass this problem with dinamic VIs loading...
Let me know if this help.... Have a nice day!
graziano