The first thing to do is tip the Soroban towards you so that all the upper beads touch the counting bar.  And the lower bead all touch the base.

Sometimes it is better to see a photograph to explain something.  The following photographs show how a Soroban is set up ready for calculating, and also the correct fingering.

Put the Soroban flat on the table and move your forefinger nail under the upper beads and moving them all away from the counting bar.

Use the thumb to 'SET' the '1' beads, which are the 4 lower ones.  This is the only time that the thumb is used.

Use the forefinger to 'SET' the '5' beads, at the top.

Take lower beads with the forefinger and NOT the thumb.

Take upper beads with the forefinger and NOT the thumb.

The pinch is just what it sounds like - the thumb and forefinger are pinched together.

This happens with 6, 7, 8 and 9 if there are enough beads.

You might like to go to this link to download a fairly large book by Kimie Markarian on the soroban.  These are the notes which Kimie made for teachers at the ATM conference when she was giving instruction on how the soroban works.

She also references the soroban to the national curriculum.

http://www.japan21.org.uk/teachers/resources/downloads/soroban.html