After your 5cm x 5cm square has been scanned in, use Photoshop to flip, twist and further adjust the pattern more. When you are happy with this, use the colour picker to do 3 different colour schemes for the batik (No limit on the number of colours used.)
Colour plan for batik
Choose the best looking colour scheme and print it out in colour. Now you have to schedule the order the colours need to be waxed in. Batik colours start white (colour of the cloth) and gradually light colours added first and darker colours added later. Next to your colour plan write the names of the colours and put them in order of lightest to darkest.