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I'm working from the PitchFactor, but it should be the same process.

… sync my Timefactor to the clock output of my sequencer in my computer …

The first place to check for MIDI clock output.  Keep in mind that some programs don't transmit clock until the DAW / sequencer is in Play / Record.  There are freeware programs (like Bome's SendSX) where you can check the sequencer MIDI output for the presence of MIDI Clock pulses [F8].

… i have to set the [MIDI CLK] ON, then connect  the midi output of my  soundcard to the pedal input and generate clock/timecode to make things work …

In the TF System –> MIDI settings, OUTPUT = THRU; CLK IN = ON; CLK OUT = OFF.  In the TF System –> GLOBAL, make sure that it's set to OFF for now.

… what about the encoder button, does that need to be Tempo On too (in normal mode) or off?

TEMPO=ON.  This is a setting saved in the preset, so check it again (or save the preset) when you switch between presets.

how do i know if the pedal is receiving clock and working on the tempo it is given?

In the System –> MIDI settings, CLK = IN will flash if the stompbox is not receiving a MIDI clock signal.  If it stays at a steady state, you're getting MIDI Clock (in the latest PF updates, anyway).  In PLAY mode (hold the right footswitch from Bank mode), tap the right footswitch again briefly.  You should see the MIDI tempo in BPM.

If everything is working correctly, you can change the tempo in your sequencer, and the TF in Play mode will display the tempo changes as they come in.  The last PitchFactor update really improved how quickly an external MIDI clock rate change will be reflected in the stompbox.