Respectfully, James Madison was a Calvinist, not a Deist. The other major author of the Constitution, Alexander Hamilton, was an Episcopalian.
Your confusion (if not merely indicative of the modern "all the founders were Deists" propaganda) is probably due to the use of the term "Deist" to not only mean those believing in a non-interfering creator (something incompatible with the Creator mentioned in the Declaration of Independence), but also independently used to describe those opposed to the Puritanical fanaticism (a philosophy well described in the 1708 Letter Concerning Enthusiasm) who clearly do not adhere to the more common modern use of the term. As such, many of the founders might indeed be described as "Deists", but such is not incompatible with the Christianity that just about every one of them, with the possible exceptions of Jefferson (who might best be described as a Christian heretic) and Franklin (a hedonistic Unitarian), espoused.
Additionally, the constition protected slavery for 85 years; it did not work well for those humans enslaved with its consent.
Perhaps Madison's response (in Federalist #42, clarifying that the intent of the Constitution was to ultimately abolish slavery, not "protect" it) to similar misunderstandings about the new Constitution might eliminate your confustion as well:
It were doubtless to be wished, that the power of prohibiting the importation of slaves had not been postponed until the year 1808, or rather that it had been suffered to have immediate operation. But it is not difficult to account, either for this restriction on the general government, or for the manner in which the whole clause is expressed. It ought to be considered as a great point gained in favor of humanity, that a period of twenty years may terminate forever, within these States, a traffic which has so long and so loudly upbraided the barbarism of modern policy; that within that period, it will receive a considerable discouragement from the federal government, and may be totally abolished, by a concurrence of the few States which continue the unnatural traffic, in the prohibitory example which has been given by so great a majority of the Union. Happy would it be for the unfortunate Africans, if an equal prospect lay before them of being redeemed from the oppressions of their European brethren!
Thank you. I have long argued that Deism as defined by the people to whom we often ascribe it can not mean what we are taught it means, particularly in school today.
Can you provide me with more on this (will look more on own later, of course)? Thank you.
Regarding Federalist #42: It is always good to have occasion to read a Federalist Paper, that has been referred to during the day, from end to end. I usually smile and learn somthing as well and this was no exception. It appears that Madison also supported a ten dollar per head tax on imported humans in addition to the importation ban by not before 1808. I notice that madison only talks of banning the importation, and not the abolition inside the states, although he hopes "an equal prospect lays before them...". He also indicated that only a few states even allowed importation of slaves; I suspect South Carolina and perhaps Louisianna, but I wonder what the other(s) was? I liked the talk of piracy and its threat in those days; I know we have piracy today, but it doesn't target container ships. Later in the essay, Madison suggests a power to coin money; it is interesting that he says nothing about Bills of Credit (banknotes).