I have a few questions:
1. Laterals do not count against the license. These can be used to help keep the number of pipes in the model lower. More information can be found here: Is there a criteria for selecting a pipe limit when purchasing WaterGEMS or WaterCAD? Inactive pipes do not count against the license either.
2. WaterCAD standalone does not use a coordinate system and latitude and longitude are not reported. If you use a Bing Maps background layer, you could get the latitude and longitude from there. See this link for more information: Reporting model element latitude and longitude.
The X and Y coordinates can differ based on how the model was created. If you used ModelBuilder or added a background before adding pipes manually, the X and Y coordinates will be based on the source file. As an example, if you have a shapefile and use ModelBuilder to build a model with this, the X and Y value for the end of a pipe will be the same as the value in the shapefile being used. If a model was built like this and you elevation data for TRex is in the same coordinate system in the GIS, the model and the elevation file will likely line up. If it doesn't, you may need to reproject the model or the source file.
3. Thiessen Polygons are generated automatically around nodes in the system. This is primarily used for some of the LoadBuilder methods. You can find more information on the properties of this in the Help documentation.
4. Since more than one element can have the same GIS-ID, you should be able to maintain this if you skeletonize the model. The following links have some information that may be useful:
Tips for improving performance of all-pipe models linked to a GIS
Keeping a Hydraulic Model in Sync with a GIS
When you are using ModelBuilder to build a model, you have options to use Label or GIS-ID as the key field as well. More information on this can be found at the following link: Using ModelBuilder to Import External Data.
Regards,
Scott