There will be a view of the crystal as seen through the video microscope attached to the goniometer. The crystal must be aligned so that its centre does not move as the crystal spins. The goniometer head has adjustment screws that move the mounting pin up, down and side-to-side.
By default the UP / DOWN movement screw and one of the SIDE-to-SIDE screws are facing towards you. If you do not see the crystal, mounting pin or glass fibre, then it must be out of frame. This is why it is a good idea to pre-centre your mounting pin, so be sure to plan ahead. Anyhow, adjust the SIDE-to-SIDE movement until you see the crystal, mounting pin or fibre. If all you see is glass fibre or copper pin, then the crystal is too high - adjust it downwards. If you see nothing then the crystal is either too low or off to one side, adjust it upwards and/or sideways. The goniometer head adjustments are pretty fine, so be careful - you are aiming to get the crystal midway on the centre line of the crosshairs. Next adjust the SIDE-to-SIDE movement for the screw facing towards you. Do not worry if the image is a little blurred at this point.
You always (unless you really know what you're doing) adjust the crystal position by moving it perpendicular to the line-of-sight of the video camera. Spin the crystal by 90° by clicking on the large "Phi + 90 degrees" button in this window:
Again, adjust the SIDE-to-SIDE movement until the crystal is centred. The crystal should be in better focus now. You are aiming to adjust the crystal position so that it does not wobble as the crystal spins around PHI. Spin the crystal another 90° and adjust again. If you need to fine-tune the height, you must spin PHI until the height adjuster faces you. Repeat the spin-adjust-spin-adjust procedure until the crystal is centred.
Important: The microscope may not be perfectly centred, but it does not need to be. It is very rare for the microscope height to be off, so long as the crystal does not appear to wobble side-to-side as it spins then it should be ok.
Expend some effort to get the crystal centred properly - it is very important. Remember: you cannot fix sloppy experimental technique after the fact.