There should not be a geometry table so there should be no problem. You will want a table that has a geometry column though. Actually,
geometry is the data type, and the column that is of that type can have any name -- the name, however, is conventionally called "geom" or sometimes "the_geom".
You use the template_postgis only when you create a spatial database:
Assuming you're using pgAdmin III,
Object browser > Server Groups > Servers > PostgreSQL (localhost:5432) > Databases
(From now on, this will be just
pgAdmin: >>> Databases)
pgAdmin: >>> Databases R-mouse-btn> New Database
That last bit is important; it ensures that the DB is spatially enabled.
Now go examine your new DB.
pgAdmin: >>> Databases > my_new_db > Schemas > public
Notice the counts for the new "empty" DB are all (0), except Functions (approx. 892), Tables (1), Views (4) -- thus, it's spatially enabled.