Allan,
With an MTS3 system, even if using one of the basic LGB MTS handsets, as far as I recall you can still toggle between Parallel and Serial control? Something to do with the "9" key I think, though it's many years since I upgraded from my old MTS2 to Massoth, I'm sure someone here can quote the details?
So even if the loco decoders ARE old serial types, you still shouldn't have any problems operating them on your current system. - the only complication is that you will be needing to switch between parallel and serial mode each time you switch to controlling one of those locos.
However, having just gone back and re-read your original question in the first post... I'm thinking we may have all strayed a little off-track here - I'm guessing you maybe already know all this and have been successfully running the locos on your system, but don't want the hassle of having to continually switch between modes when switching locos? If that IS the case, then (aside from Greg's suggestion of swapping out any old serial decoders for more modern types) I would think your best bet is to get yourself a Massoth Navigator handset, which will work with your MTS3 central station and will allow you to store the details of each of your locos permanently in the handset - so when you select the loco address, it will automatically go to either serial or parallel mode as appropriate to the stored details for that loco.
Jon.