Amir,
Make sure to split your centerlines where ever they intersect. GeoRAS will still run, but there is the chance that it will screw up your distances if you dont split them manually. As long as you use the snap tool to overlap the vertices, HEC-RAS should still create the junction.
As for the node outside the terrain error, I assume you are using the DEM from your previous post as your terrain data? If so, it seems there may be a bug when using georas with DEMs. Several of my coworkers have experienced similar errors even though the spatial reference is correct and the lines are quite obviously within the DEM boundary. It doesnt happen all the time though so we havent yet pinned down what the issue is. You can get around this by clipping down your DEM and converting it to a TIN.
Hope this helps.
It will only auto-generate the junctions if you turn on vertex snapping and snap the end vertices. Double check to make sure you have those points snapped together.
Failing that, its just as easy to turn on "move object" in the HEC-RAS geometry window and just move the end vertex of your tributary stream to overlap the receiving stream. This will split the reach at that location. You will have to manually input the junction data though(distances and such).