It sounds like you need to use the '/nui minimap' option to enable nUI's management of the minimap. If you do that, then the minimap will be in the middle instead of in the upper right corner.
As for recount, when you install it, nUI will automatically put it in the information panel that's in the bottom right of the dashboard... there's a red button there that says "Map" -- click it to switch to Recount or Omen.
There are also plugins in the nUI download area
http://www.wowinterface.com/downloads/cat125.html which allow you to put Omen and Recount in the same info panel, or to have them automatically switch between Omen and Recount based on whether you are in or out of combat.