Your Rapture is looking pretty similar to mine. Mine was split out by the Installer so your locations are valid. I'll explain a bit more (from what I know).
C:\Program Files\Cakewalk\Rapture (for x64, x32 in "Program Files (x86))
- Documentaion
- LFO Waveforms
- Multisamples
- Resources
- Tunings
--- Rapture.dll (DXi or VSTi (?))
--- Rapture.exe (Standalone)
(I've got my VSTs (x64 and x32) out under a common VST location. Can't remember if I copied them or prompted during install).
C:\ProgramData\Cakewalk\Rapture
- EG
- MIDI
- Programs
--- Elements
--- Expansion Pack
--- programs.lst
- Sample Pool
- SG
Expansions will come as Installs or Unzip/Copies. They'll typically come with instructions but depending on what they have in them .prog are deployed under Programs, .wav and .sfz are deployed under Multisamples.
To make your new Expansions visible you've got to regenerate the programs.lst file by opening the Program Browser from within Rapture and pressing F5.
Do you have the Documentation folder? Better/more info in both the .chm and .pdf. They explain the File Organization and more ... briefly:
Documentation\
- Documentation folder. Release Notes, User Manual and Registration information.
LFO Waveforms\
- LFO Waveforms folder. All factory LFO waveforms. User-defined waverforms can be stored here as well.
MIDI\
- MIDI folder. All MIDI Learn data.
Multisamples\
- Multisamples folder. All factory wavetables, multisample definitions and sample collections.
Programs\
- Programs folder. All factory presets/programs. Rapture will point to this folder on Save...Program.
Programs\Elements\
- Elements folder. All factory elements. Rapture will point to this folder on Save...Element.
Sample Pool\
- Sample Pool folder. Project/Demo song specific samples.
Tunings\
- Tunings folder. All microtuning and alternate tuning files.