I've recently come to the end of a long journey in converting my Macbook Pro into a recording studio. After all my trial and error, here is a breakdown of the problems I came across and solutions to fix them.
My stuff:
61 key Novation X-Station (connected via USB, powered by wall socket)
-includes 2 XLR/ 1/4" inputs and outputs
MacBook Pro with OS 10.5.1 (Leopard)
2.16 GHz Intel Core Duo
Intel Hi-Def Audio card
Condenser Microphone
This tutorial works for Logic Pro and is very similar to ProTools.
I originally installed Logic Pro onto a Powerbook G4 which runs on Power PC chips. It wasn't powerful enough to run Logic, although the Midi drivers and Core Audio drivers worked perfectly for recording Midi and analog audio through XLR or stereo jack.
I upgraded to my current Intel MacBook Pro and made a clone of my computer settings from the Powerbook.
and nothing worked anymore. I had to buy the bootcamp upgrade for Logic Pro to adapt to Intel. The Midi drivers that came with the X-Station wouldn't work and were referencing drivers installed on my Powerbook. Everything was a mess. The Core Audio driver wasn't working properly for any 3rd party inputs.
I was in the middle of post-production with Tucson Underground and couldn't wipe my computer clean. Luckily Apple wiped my hard drive when they fixed my DVD drive. I decided to upgrade to Leopard shortly after.
My computer was thus wiped of all old audio drivers for the MIDI on the X-Station and the Core Audio drivers. I re-installed Logic Pro and re-installed the X-Station drivers, I also went online to
Novation and downloaded all the MIDI updates for the past few years. Once this is complete, do the following to connect your MIDI device and connect your audio drivers.
Go to your Utilities and open the "Audio MIDI Setup", make sure your MIDI keyboard is connected via USB and choose the "MIDI Devices" tab.

Hit "Add Device", if your device doesn't show up, hit "Rescan Device". Now choose the "Audio Devices" tab.

Select your device as the "Default Input" because of this, your MIDI keyboard can be used as the input and also output to the speakers, i.e. you can monitor what you are inputing into your computer. Therefore I leave my Default Output and System Output as my built-in.
Next, go to your System Preferences and select Audio options. Make sure your MIDI driver is your selected input as well:

Although it seems logical, I put the headphones (built-in output) as my output. I have an output to monitors (speakers) on my MIDI which is much better. If you have MIDI as your ouput as well, your USB will get bogged down and run slowly.
Now you're ready to open Logic, with your MIDI turned on. And go to Preferences> Audio :

It's imperative that your Core Audio driver is selected and you choose X-Station as your enabled driver.
To Play MIDI: select a MIDI track and under I/O select a synthesizer for example. Play away. Notice that on the Transport window, it is receiving MIDI information for each note you play. Record enable it and play away.

To Record Guitar or Vocals: slect an audio track, select the input that your instrument is plugged into on your box (ex: Mbox, Mbox2, the X-Station). Record enable it so you can monitor what is coming in. Select a Plug-in, GuitarAnpPro for example.

Set up a quiet space that is sound neutral (low acoustics) and get some great headphones if you want to record vocals. I use my closet, smells great.
Hope this helps. I'd love to get some feedback.