Hi Joan,
That's several questions... let's look at each.

Hello, can anybody tell me the best way to récord tracks in song mode to cubase.?

If you have recorded a sequence in the Motif XF you can simply use Cubase to Import all the data from your .X3A ALL data file. Please see this artlice: MOTIF XF SONG IMPORT
This allows you to simply open the file in Cubase, then you can better deal with the playback of MIDI data, and the rendering (routing/recording) of the audio. It is these routing decisions that can greatly impact the quality of your final results.

Is better do it in mono or stéreo?

That depends. Certain sounds, certain effects must be recorded as stereo audio in order to function properly. That is a decision you make, as Producer, on a per Part basis... a bass sound for example does not benefit necessarily from recording it in stereo, but a sound with a stereo effect (say an organ thru the Rotary Speaker Effect) even though the organ itself is mono, the effect requires stereo to "rotate" - it's not rotating if it's not recorded in stereo.

Is better record with the outputs L and R like audio files through an sound card like audient id14 or is better récord the tracks like midi tracks with USB conector or firewire with FW16E?

Certainly the FW16E will give pristine 24-bit audio of the highest quality. If you have a system that can do FireWire, definitely do. It will all depend on what you want to achieve. Recording everything to stereo is certainly a workflow that give great results. You will have to decide which is the best route to take for the project you are working on.

How can I get the best quality of sound of muy motif?

Your audio results are only as good as your audio path. As you experiment with recording methods you will learn to get better and better at the process. We have several guides with tons of tips and tricks here on YamahaSynth.com under Synths > Motif XF.

Motif XF Routing Parts via FireWire