APP_3V3 is connected to the eval board's 3.3V rail.
EMU_3V3 does not actually seem to be connected anywhere, from what I can glean from the schematic (well, the two connectors are connected together, but that's it).
You can get the answers you're asking about from looking at the (frankly pretty horrible) schematic of the eval-board.
Fortunately, the schematic is saved as a vector-file, rather then images, so you can search for net-labels in the PDF. The only place
EMU_3V3 crops up at all is on
Note that this is a pretty freaking terrible schematic. There are multiple power nets, that are connected together. As such,
EMU_5V are really the same net. The same is true for
APP_3V3, which are also all tied together.