So, I've been trying to connect to GeekShed on start-up of mIRC (No problem here), but how can I connect to Freenode (for my other channels) on startup?
I'm sorry it took so long to get back to you. What you'll want to do is go to options, and after you connect to geekshed you'll go over to servers, double click freenode, and when it takes you to the connection page check the box for start in new window. That way you can have both up at once. As for auto-loading channels, you can set your favorites to respond by server instead of having the same set load for each server you join. I'm a bit picky about my channel ordering though, so I usually just write scripts for it.
If you'd like to make a channel script, that lets you join a set of channels when you type a command, drop the following line into your aliases, with your channels separated by comma (no spaces)
/chanset1 /join #Channel1,#channel2,#etc
For example
/chanset1 /join #belltree,#treeofbells,#bellsoftrees
All you'll have to do is type /chanset1 when you're all booted into the server. You just make a separate chanset for each list of channels you want to join based on server. This way, you can order your channels to make it feel more natural, or group channels a specific way that may be easier for you to keep up with.
Aliases can be found at the top, it looks like a white notepad.