I haven't had any problem entering SOS's into SA. Right click on your 'player green dot' to get create waypoint here, add the coordinates they will appear in the 'water' wherever the sos happens to be located.
You just need to make sure if you're entering the sos that you are in the correct facet, so enter trammel sos's in trammel etc. If you are sitting in your house in malas or fel or tokuno and try entering a Trammel sos it will put it in whatever facet you are in at the data entry time.
Just sucks that we do not have the 10 custom icons we had in KR nor the ability to resize the icons that the 'default' uses. At least in KR for most of the icons you had the option of small medium and large for most things, and could at least change the color. All I have now is a mess of green dots on my map and no idea what each represents.