Follow all suggestions that you agree with and document those you do not agree with and attach a clear explanation of why you disagree with them (possibly offering an alternative if you understand what exactly the referee was unhappy with in the original version or asking for clarification if you don't). Remember that it is your paper and you want to have it the way you think is right more than you want it to get published, so don't forget yourself when listing the parties whose opinion should be taken into account. Normally, a compromise satisfying everybody can be reached in finite time but it may require more than one iteration. As long as you stay polite and make your point of view clear and substantiated, occasional disagreements with reviewers and editors constitute a normal part of the publication process and are nothing to be afraid of. And, of course, try to meet the deadlines or at least inform the editors in advance when you cannot.