The only thing I would have done differently is not waiting for several weeks. Configuring a wireless network is messy and difficult. The easiest way through the mess is one small step at a time. Set it up with all defaults and no security. And get it working. Many people realize that security is important and try to set it up fully secured in one fell swoop. They pull their hair out for days trying to reconfigure the security when really the network wasn't working in the first place. When it is working (as yours is), immediately start locking it down one feature at a time - encryption first, then MAC address filtering, and finally, turn off SSID broadcast in the access point.
You can do these things manually from the setup pages of your router. Personally, I do these things manually rather than rely on some script on the installation CD. I would bring the laptop downstairs and set it beside one of the wired desktops. That way you can access the router's setup pages from the wired system even after you munge something in the passphrase setup or mistype a MAC number, goofs which are easy to make but once made make it impossible to reach the router again from the wireless system to fix the mistyped item. Once you get the laptop set properly, you can go back upstairs and configure the wireless desktop. It will go much faster for the second one as you will have learned from all your mistakes on the first one (mistakes which you didn't have to run up and down the stairs many times for...).
Okay, here's my problem, I just set up wireless networking in my house a few weeks ago, we have the router downstairs with ethernet cables running to two side-by-side desktops, my desktop upstairs receiving the signal via USB wireless adapter, and my notebook receiving via built-in wireless card. When I first set up the network, I was more worried about actually getting it working than setting it up 100% correct.
Basically, after the linksys network has been set up is there any way to go back and set it as secure? I have firewalls on the computers of course, but nonetheless. Please help, I really don't want to go through and run that thing again, it doesn't detect the desktop as connected to the internet, although it has internet access!
Sorry for the long post.