Flashman is not amoral, but immoral. There is no doubting that he is aware of the folly of his doings and the harm that they can cause, he simply chooses to ignore this. It is this understanding that is the difference between the two.
When it comes to rogering everything in sight, he is most definitely aware of the consequences, as can be seen from what happens in "Flashman's Lady" when Don Solomon Hasman catches him in flagrante delicto with a lady of ill-repute. It should be noted, however, that his ability to mount just about anything in a skirt saves his skin on several occasions, most notably with Queen Ranavalova and Maharani Jeendan. Of course, the counterpoint is that it also nearly kills him on several occasions as well.
Any student of history can gain a very good understanding of Victorian society from these amusing and (mainly) factual accounts of major historical events.