There are a few things that I do not understand in your post. It would also help to know which version of Trainz you are using.
I can lock the layer out, but when trying to add an asset the baseboard overrides and will not allow the asset
Locking a layer only prevents you adding assets to that particular layer, not to the baseboard. If your "active layer" is not locked than you can still add assets. In Trainz Plus and TRS22 Platinum the "active Layer" is the selected layer in the Layers Palette (if you are using Surveyor 2.0) - it gets harder to explain if I do not know which version of Trainz you are using. Are you using Surveyor Classic (all versions of Trainz) or Surveyor 2.0 (an option in Trainz Plus and TRS22 Platinum only).
The baseboard itself is not in any layer and can be edited, deleted and added to regardless of the locked status of the layers.
I have assign the asset to a category in the route layer
I have no idea what you mean by "assign the asset to a category" - what category?
Additionally when adding assets to the route they don't save.
The most common reason for that is confusion over
Route Layers and
Session Layers. Anything placed in a
Route Layer (such as in the layer named "route-layer") will be saved when the route is saved. Anything placed in a
Session Layer (such as in the layer named "session-layer") will only be saved when the session is saved. You of course can add as many layers as you like to each.
So if you have placed something in a
Session Layer but only save the route then it will not be saved.
May I recommend some primers of these subjects -
How_to_Use_Layers and
Routes and Sessions.