"Siéntate bien", "estáte quieto"

You can say:

• sit up straight ←
• sit properly
• sit still (=estáte quieto)

"poneos en fila"

You can say:

• line up 
• make a line

You wouldn't say "queue" (you queue at a supermarket, for example).

"leed el enunciado"

You may simply say "read the question instructions".

wax crayons

The full name for "ceras" is "wax crayons". However, in a classroom setting, it is OK to simply call them "crayons". 

punches (punzones)

In infants, a typical activity is to punch the paper. The tool you use might be called a punch, because you punch with them. 

However, these are not really typical in a British school context. 

You may also use a hole punch.