Instructions in writing are always the best way.
A Site Instruction can be required on site or yard for all sorts of reasons such as safety, access, errors, rework, intereference or coordination issue.
The instruction is best given in writing and if this means a change to the contract then the change procedure shall be followed first.
Site Instructions shall be recorded in a register which shall be mainained and discussed between the parties. The number of instructions can provide a trend for site issues and their causes.