Karnius, I just started here a few weeks ago as well. =) I hope your stay ends up being as great as mine has been, these blokes have done a great job, ne?
I don't know anything about that web installer, but these are the steps that got me up and gaming nicely:
1) I downloaded the retail FS2 CDs from FreespaceZone (Google it, the site owner has requested no direct links). This is the ideal base to install the rest of FS_open off of.
2) Run FS2 retail once, make sure all the options are set as you like. PATCH the game to 1.2. You can get the patch file from Volitions website.
3) Download all the ,ediavps here:
http://www.hard-light.net/forums/index.php/topic,39905.0.html. The files you will NEED are mv_zpack.rar, mp-710_effects.rar, and mp-710_models.rar. However, I would get mv_adveffects.rar and mv-710_adveffects.rar as well.
4) Create a folder called "mediavps" without quotes in your freespace directory. (Usually c:\Freespace2)
5) Download the FS_open Launcher here:
http://icculus.org/~taylor/fso/testing/Launcher.rar
and place the Launcher.exe file in your root Freepace 2 directory.
6) Download an FSO build, the best one to start with is 3.6.9rc7.9x here:
http://icculus.org/~taylor/fso/testing/rc7dot9x.rar. Place the fs_open_3.6.9rc7dot9x.exe file in your root FS2 directory.
7) Make a shortcut on your desktop and point it to the Launcher.exe file in your FS2 root directory.
8) Before I forget, make sure to download an install OpenAL! Get it here:
http//developer.creative.com/articles/article.asp?cat=1&sbcat=31&top=38&aid=46&file=OpenALwEAX.exe.
9) Copy all .mve files from your "retail" FS2 CDs into Freespace2\data\movies Make sure to get them all.
10) Open the launcher. Now, there are a few options people say are quintessential. You can probably find more out about this here:
http://www.hard-light.net/wiki/index.php/Command-Line_Reference.
I know I play with this in the custom command line textbox and all options on:
-no_emissive_light -ambient_factor 0 -spec_exp 5 -spec_point 1.0 -spec_static 0.4 -spec_tube 1.0
Make sure to go into the Video tab in the launcher and configure that. DO NOT use D3D! Use OpenGL. It's all that's really supported anymore, as I found out the hard way. XD
11) Go into the tab at the top of the Launcher called "Mods" and set the mod directory to the mediavps directory.
12) Hit Apply and then Run to runthe game! =)
That should do it. You won't need the Cds to play.
EDIT: I don't know about the HOTAS stick (what is that, anyway... people keep talking about it...) but YES, Freespace 2 supports both Absolute Throttle axis and Relative Throttle axis.