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well you can understand it in different ways. we know that in a conducter when electron flows the electron hop from 1 atom to the next to transfer beacause electrons are free not the atoms, as a result you have an equall and opposite current called conventional current that is due to flow of +ve charges. this type of study is very common in field of electronics, to understand it u can take water in straw or somthing narrrow, when you turn it again and again the bubbles and water move in opposite direction according to the situation, so same is the case of electronic and conventional current. you can also understand it in the process of electrolysis in which the current is actually the transference of some poitive ion which in turn was the result of increase or decrease of electrons from a particular part of the cell in which the procss was being carried :) hope u'll get it.
yea.. but don't think that protons are flowing in the opposite direction.. protons are stationary well inside their nucleus