This adding is a bit confusing if you ask me, but there are a few pointers here.
First, the easiest way not to confuse yourself, is to choose the option to use the LinuxMCE folder structure when asked. This means you have to reorganise your media into the new folder structure it will create for you, but it will mean that your PC will play nicely with the rest of the media and present consistently.
Pretty much as soon as you have done this, you should see the folder structure appear on your Windows share - if this doesn't happen then you have come permissions or connectivity issue.
Connectivity - I would suggest that you create a specific share (don't use $ to hide it) for it to use and create the folder structure under rather than letting it suggest the default admin shares like C$ and D$. Make sure they can each ping each other and that the Windows machine has a valid DHCP address. Try using the Windows machine's Network Neighbourhood to browse back into the Core's hard drive as this will confirm that higher layer network protocols/functions are working (CIFS/SAMBA). If you browse into My Network Places/Entire Network/Microsoft Windows Network, you should see a LinuxMCE "domain", inside that, you should be able to see the profiles and copy files back and forth. Note: it sometimes takes 30 seconds or so to display the icon for LMCE.
Permissions - Make sure that you set the Share to have Everyone - Full Control permission, and the NTFS permissions of the folder itseld to allow full control for the account you intend LMCE to use, if it is a computer in a domain. Depending on OS version, if the machine is just in a workgroup, you may not have the option to set NTFS permissions, in which case set the Share itself to have full permissions only for the account you intend to use for LMCE.
If all this is right, you should see the folder structure appear, if not check in the Windows security log under Computer Management for security audit failures to do with this account - the help link will tell you if it is because the password is wrong or account doesn't exist, locked out, etc.
At this point the media service should start scanning the folders and creating an index in the database of your media. This is slow, expecially if it has to do a lot of work, like creating thumbnails for photos, or downloading stuff. But browsing around the folders in Windows you can often see if it is doing something. Or you can use Computer Management again, under Shares, Files or Sessions and keep hitting refresh - you should occasionally see a connection from the LMCE device to a file as it processes it.
I understand that from the Admin website there is a process (described in another post) that you can manually point at a share/folder and force it to scan again. If it has already found your share and you aren't sure if it is doing anything, you could either delete the share from the admin console and let it find it again, or use this function to force it to start again.
Finally, from what I can see, it only seems to present newly scanned media to you to select from the media menu, after it has completed scanning an entire (single) folder and moved onto the next - purely anecdotal - in which case, if you have some very large folders, it may take a while before you see anything.
Oh, finally, finally! Lots of people see to get stuck on this one (I did, and have seen other posts) - the video and audio browser defaults to sort/searching by "title" or "performer" rather than filename. If you have a lot of media that hasn't got attributes set, then they will only appear if you choose to sort/filter by filename.