I have done this several times with and without a Bahtinov-mask. In the Focus tab you simply click the Loop button and let Ekos take pictures. Ekos will then calculate the HFR either of the selected star or of all stars in the FOV. When you move the focuser manually (either via a remote control or by turning the focus knob) and wait for Ekos to take the next picture, you can monitor the HFR and consider your telescope focused when the smallest HFR is reached.
When using a Bahtinov-mask you can disable the star detection in the images (by clicking the most right button inside the button bar at the top left of the image) and simply consider the telescope focused when the spikes align as they should.
ASI1600MM-Pro Cooled and filter wheel with a SkyWatcher Esprit 80 ED on a SkyWatcher HEQ5-Pro
ASI1600MM-Pro Cooled and filter wheel with an 8" TS Ritchey-Chrétien on a SkyWatcher EQ6-R