A right way? Probably not. I prefer this way (placing them on the schematic as components), so that they are required during layout, so you don't lose space forgetting some.
I haven't found default settings, but it's easy enough to filter them, e.g.,
PCB Filter Panel > Name Like 'TP*', apply
PCB Inspector Panel > select Designator link, tick Hide
Or go to PCB List, Display Only: Components; sort the listing by Name; select TPs; fix properties on Inspector Panel.
Can also select/enforce TPs by selecting the pads (filter: IsPad AND (Name Like 'TP*-1'), or select from Pads on the List) and ticking Testpoint on Top/Bottom. The Testpoint Manager dialog doesn't always select the TPs you wanted.
Tim