Homeworld 3 Niagara Systems such as engines or RCS VFX effects are using the coordinates given by a Houdini Point Cache Asset.
To modify a base game effect to fit a ship you are rigging, you would need to edit his Point Cache. Except you will notice that you can't do that in the editor. Doing Right click > Export on the asset will give you a binary "HBJSON" file, containing the list of parameters that defines the effect coordinates in a non human-readable format.
In order to edit this file, I made a parsing and encoding tool allowing for HBJSON -> JSON and JSON -> HBJSON conversion. The workflow would then be to export the HBJSON of the effect you want to edit, convert it to JSON using the tool (you want to edit the Cd (= coordinates), the Pscale (scale) and the "InitialSpriteSizeX/Y" of the data points. You can then convert you edited JSON back into HBJSON and import it in the editor.