Councillors must not interfere with the work of the clerk. The clerk is the executive arm of the council, and is responsible for putting the council's decisions into practice. There may well be occasions where councillors will work with the clerk on a project, such as the organisation of a local event. But both individual councillors and the whole council must respect the clerk's role.
Where the behaviour of a councillor is creating problems for the clerk or the council, it is very much a matter of judgement how things should be handled. In this situation, the clerk will often need support from the council. The chairman does not have any special status derived from legislation, but often the seniority attaching to the role is seen as a justification for the chairman being the person to tackle the issue. The role may make an intervention more acceptable to the misbehaving councillor.
What is said by the chairman (or any other individual councillor) cannot be regarded as an instruction. It is advice on the roles of the various parties and on the council's attitude to the actions of the individual. Clearly it is quite tricky to make this work, but it is a challenge that does arise frequently.