Both is possible: own folder structure for wrapped plugs, or leave them in the folder along with the native.
Automap wrapper always and only puts the wrapped plugs in the native plugs folder, so you have to manually move/copy your thousand plugs... X1 usually scans the automap plug first, but I don't want to rely on host routines scanning/identifying multiple plugs with the same VST-ID in folder structures...
I wrote my own plugin manager app in vbscript/hta to automap/organize plugs into categorized subfolders and built a vst2x32 and vst2x64 plugin folder structure with automapped and, if needed jbridged automatically on demand (when I install new plugs)
I install plugs and never touch the installed files ever again. Instead, I run my manager, sort a info file into the proper category and rebuild my plug folder structure.
Somehow the small automap dlls are like links to the native plugs...
I own multiple daws like Cubase, reaper, fl studio, live8 soon, and every host shows plugs sorted like they are in the folder structure (besides fl studio, bummer)
Always properly sorted and organized. No doubles...
(I managed to rename wrapped plugs within Cubase, so they don't show as "... (Automap)" in the app, which is necessary for Cubase and its vst3preset system... you usually MUST NOT rename automapped dlls!)