Rather than Methylene blue, It would be better to try some other medication. It wont help Ich at all and the best treatments against finrot and ich is keeping water quality good. Also, raising the temperature to over 30C or 86F will help get rid of Ich but it will re-appear if the fish are stressed and the water is not good.
Methylene blue is really suited for hospital tanks where it will not harm the biological filter of the main tank as any damage to the biological filter in the main tank can cause many more serious problems then just fin rot and ich.
What is the problem with internal parasites?
Nim