Good question Chris.
I would prefer your first option and make files like SubRES_NewTechs-<SectorName>.
Remember that VEDA still needs to know the sector when it encounters any new technology/commodity. In the case of base year (BY) templates, this information comes from the file name. In SubRes files, it comes from the sheet name. But you can have several sheets for the same sector by using an "_" after the sector name. For example, if ELC is one of your sectors, you could name sheets like ELC_Nuclear, ELC_Fossil, ELC_Renewable etc.
In principle, you could also include new techs in the BY templates without much of an issue provided you have only one template per sector. But if you decide to add more regions (super-regions, actually), then you will need to copy the same set of techs across multiple workbooks, which is clearly undesirable. The other reason I would recommend the first option is that, generally, one would edit the new technologies more frequently compared to the existing technology stock. If new techs were in BY, then all the existing techs would need to be reprocessed each time you change/add new technologies.
With multiple people working on different parts of a model on an ongoing basis, I would set up a central location for the "official" version of all templates. This could be a common drive on a network or even a dropbox folder. This could be supported by a google doc/Springpad/Evernote tracking system where sector/region analysts maintain a log of their updates. One advantage of using dropbox would be that it would keep previous versions of files automatically. Otherwise you can ZIP the entire set of templates periodically.