In act one of The Crucible, Mrs. Putnam and her husband visit Reverend Parris's home and begin discussing the arrival of witchcraft in the community of Salem. When Rebecca Nurse arrives, she warns Reverend Parris and the Putnams that they should not immediately start blaming witchcraft as the cause of the recent events. Rebecca insists that there is "prodigious danger in the seeking of loose spirits" and would prefer the community members search among themselves for answers before jumping to irrational conclusions. Mrs. Putnam, who is very much jealous of Rebecca, responds by saying,

There are wheels within wheels in this village, and fires within fires! (Miller, 35).

Mrs. Putnam is essentially challenging Rebecca's perspective and believes that there are hidden, unknown spiritual explanations to the sudden illnesses. The connotative meaning behind Mrs. Putnam's statement correlates to the truth behind the witch hunt. In reality, the witch hunt is fueled by greed, jealousy, and vengeance. As the play progresses, certain citizens seek revenge for various reasons by accusing their enemies of witchcraft. The "fires within fires" are essentially the burning grudges and grievances between citizens, which plays out in Salem's courtroom. 

The quote in this question comes from Act I and is said by Mrs. Putnam when she is arguing with Rebecca about the cause and the reason for her many miscarriages. Mrs. Putnam clearly points towards supernatural reasons for her repeated inability to have another child, and she looks towards others and their successful ability to have children as proof of this. When Rebecca tries to calm her down and suggest that there might be other reasons for her ability to have more children, note what Mrs. Putnam says:

You think it God's work you should never lose a child, nor grandchild either, and I bury all but one? There are wheels within wheels in this village, and fires within fires!

Mrs. Putnam therefore uses this quote to point towards the existence of the supernatural and to try and explain the unexplainable events that are happening in this village. However, at the same time, ironically, her words could be used to explain the whole witch hunt and the very damaging events that happen in Salem. To the audience it becomes clear; there are wheels within wheels within Salem, and these hidden motivations and undisclosed petty jealousies are the real driving force behind the witch hunt, far more than the actual existence of any witchcraft. Miller therefore uses this quote to point towards the real reasons behind the witch hunt and how human emotions such as jealousy, revenge and greed, were able to masquerade as genuine Christian piety and an attack against the devil.