I'll try to deal with your issues one by one... with luck, others will chime in soon, but it takes time (usually allow 24-48 hours) for people to see a post and, if they have the relevant knowledge, post a reply. ;)
1) I've never used desktop gridding software, even with Surround. I rarely, if ever, maximise a window if it's not a game... and my habits haven't changed with Surround.
Matrox hide Powerdesk away really well. To this day, I still have no idea how to actually get it from Matrox's site directly. It is available for download from a couple of the 'download aggregator' sites, but whether or not you trust those is up to you. There are a few other alternatives, however:
Acer GridVista bundled with Acer laptops for years, this allows you to 'grid up' your desktop - I've personally never used it, but people have reported success.
UltraMon is one of the two programs that reportedly work for taskbar management, etc. It does cost money, but there is a trial, so it might be worth a shot.
DisplayFusion is what I use to control my dual-screen system where I have one screen landscape and one portrait (nVidia drivers handle that abysmally). The free version is quite limited, the costly version better.
You'll probably better try GridVista first, see if that can solve your most significant issue - that of the stretch-maximise.
2) I don't think you have that level of control of the system tray etc on the taskbar in any application I know of. AMD (reportedly with Catalyst 12.2) allow forcing of the taskbar to the centre monitor in EyeFinity... if nVidia take Surround more seriously with the release of Kepler, we may see similar advances with nVidia Surround.
3) It's not SLI itself that breaks Aero Peek - it's Surround. The 'workaround' is to move your taskbar to either the right-hand side or left-hand side of the Surround array (so a vertical taskbar) but I hate that, so just live without Aero Peek. There is no other fix as far as I am aware.
4) Vertical Sync may be forced on in the nVidia Control Panel. Under the 3D Settings section of the Control Panel, go to Manage 3D Settings and check what is set in Global Options for Vertical Sync (should be the option at the bottom) - if it's 'Use 3D application setting' that's fine. Or you could force it off. I prefer to run with Vertical Sync forced on, because that eliminates tearing, which drives me insane when gaming. I'd rather live with the FPS hit than with tearing on the screen. ;)
5) Lots of games have support for SLI... far less have support for Surround. Surround is a 'niche', so even many of the big-name games won't support it - often, you're more likely to get an indie game working than you are a big-name game. It's a bit sad, but it's a lot like widescreen was a few years ago - when widescreens came on the market, almost no games supported them - even many developers said they would never support widescreen because it was "cheating"! Mass Effect 3, last I checked, ran on a modified Unreal Engine 3, which is the current bane of any Surround/EyeFinity gamers life. The engine was designed by Epic to only really cope with 16:9 aspect ratio (at least that's their excuse) and it treats any monitors narrower than that in a 'vertical plus' manner, and any wider (like Surround) in a 'vertical negative' manner. Which is a bad thing... a very bad thing. Thus, a lot of effort has gone into fixing these issues on popular games (like the Mass Effect series) but it takes time, and sometimes the fixes can be a bit... finnicky.
6) For bezel correction, monitor angles etc... it's going to all be your personal preference. I, personally, use a bezel correction of 152 pixels for each set of bezels. Any less (even by a few pixels) and I can detect that it's not lining up and I feel sick. I recommend getting a sheet of A4 paper or something similar that has a straight edge and is opaque(ish) and using that to help you line up the roads that calibrate the bezel correction during setup. Monitor angles... hm, I probably have mine at 20* off parallel to the centre monitor, with the centre monitor further away from my eyes than I do on a 'normal' single monitor setup. However, the distance is partly because the desk I use for Surround is very deep.
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You have embarked upon a rewarding path for gaming, when you get it all to your liking. But it can be a bumpy road to get there. I'm sure the rest of the forum will help as much as possible. ;)