If I understand your question, yes, the position of the clitic can change the meaning of sentence, although there are not many situations where 1) you can choose between enclisis and proclisis and 2) the choice is material to the meaning of the sentence.
There are situations where the choice between enclisis and proclisis is arbitrary, for instance, infinitive clauses introduced by a preposition (except a and com):
Não gostei de o ouvir.
Não gostei de ouvi-lo.
There is no change in meaning between the sentences. There are other situations when the choice is arbitrary.
But let's get the more interesting (but rarer) cases, where the choice exists and is not arbitrary. When you have a pre-verbal constrastive focus (usually with an adverb, but not necessarily), you use the proclisis. These are more or less equivalent to cleft sentences. However, this pre-verbal constituent might also have a topicalized reading that can be triggered by the use of the enclisis. Example:
Dificilmente o vejo daqui. (I can hardly see him from here/It will be difficult to see him from here).
Dificilmente, vejo-o daqui. (I see him from here with difficulty).
Muitas pessoas se manifestaram. (It was many — not few — people that protested).
Muitas pessoas manifestaram-se. (There was a large group of identifiable people that protested).