Here's what I (and I think many others) do to use the X3's processing and recording capabilities as well as take advantage of plugin processing. For purposes of this illustration I will talk about using the Pod Farm plugin, because it uses the same tone files as the X3 - meaning you can obtain the same sounds whether you are using the X3 for live play or Pod Farm for post-processing.

1) Select a patch on the X3 that has the basic tone that you want to start with for your guitar part. Monitor your tone/playing using the X3 (headphones or studio monitors). You are not committing to any specific tone/sound at this point - you just want something representative as a starting point.

2) Connect your X3 to your computer via usb. Start your DAW. Turn OFF monitoring in your DAW. Make sure your DAW is configured to use the X3 and its ASIO driver as the audio input/output device.

3) Arm a track for recording. Select a dry (unprocessed) signal from the X3 as your track's record input source. This will probably appear as option 7 (Tone 1 Dry) or 8 (Tone 2 Dry) in the Record Input selection menu for the track in your DAW.

4) Start recording. You will hear your wet, processed signal directly through the X3 Outputs. Meanwhile, your DAW is recording the dry signal. The record level will probably seem low - this is OK. While recording the track do not activate any plugin on the track in your DAW.

5) When recording is complete, put your guitar away. Use Gearbox with the X3 to transfer the tone file for the patch that you just recorded to your computer. Store this tone file into the folder (or any subfolder) on your computer where Pod Farm is installed.

6) Select the track you just recorded for playback. Activate Pod Farm for this track. Navigate the Pod Farm tone library (computer folders) and select the tone/patch that you just transferred form the X3. Start playback. Since the X3 is also your DAW's output device you will again hear the  sound through the X3 outputs. You will hear the exact same tone that you heard while recording, but this time the tone is being produced on your computer by the Pod Farm plugin rather than by the X3 itself.

7) Continue to develop your song, recording other guitar parts in the same manner as above. Tweak your tones further in Pod Farm any time you like as your song develops. Since Pod Farm is using the dry track as its input, you have full flexibility in tweaking your tone - you can develop it completely from scratch again if you want. No need to re-perfom that perfect take just because you want a different tone.

8) When your song is complete, export the final tone file(s) from Pod Farm to your computer folder. Then use Gearbox to transfer the tone to your X3 so that you can perform the song live with the final tone/sound of your recording.

Let me know if there's anything that's not clear, or if this method doesn't seem to work for you. We may be able to tune the approach to suit your needs. Depending on the processing power of your computer you will eventually reach a limit in how many instances of Pod Farm you can run simultaneously during playback. There are strategies to deal with this.

EDIT: Of course you can adapt this method to use any plugin, but if you use anything but Pod Farm (even if you use Pod Farm 2) you will not have full (2-way) file transfer capability with the tone files.