Ah. In the (lack of) style of the FAQ then
I'VE GOT A LOT OF BANDWIDTH/TIME WHAT SHOULD I DOWNLOAD FROM THE FTP? If you have the time and bandwidth the best thing to do is to download all the the vp files from the FTP rather than just downloading a few of them as this makes it much simpler because you can then replace all the HotU files in your data folder.
To do things this way you should get the following VP files from the FTP.
# root_fs2.vp
# sparky_fs2.vp
# sparky_hi_fs2.vp
# stu_fs2.vp
# tango1_fs2.vp
# tango2_fs2.vp
# tango3_fs2.vp
# smarty_fs2.vp
# warble_fs2.vp
Look in your Freespace2 folder. Take all the files with the extension .vp and drop them in your data folder. Rename your data folder to Data-HotU
Make a new Folder and call it Data. Go into Data-HotU and copy the players folder into Data.
Move all the .vp files you downloaded into the Freespace2 folder.
If you plan to use FRED you should download
this file, make a folder in data called freddocs and extract the contents to it.
That's it. To all intents and purposes what you have now is exactly the same as the retail install of FS2.
(Actually I tell a lie. I think you may also have to download a couple of .reg files and add them to your registry to set things up correctly. However I believe the SCP launcher will also set those up so it shouldn't be a problem).
Now you basically install FS2_Open in the same way someone with retail would do it. i.e shove the media files, launcher and exes into the freespace2 folder and run the launcher.