In English grammar certain verbs like suppose and believe, referring to thought, can have a negative marker attached to them without affecting the scope of negation. For instance, the not in “I believe he’s not coming” can be attached to believe itself to give “I don’t believe he’s coming”, with no change in the truth value assigned to the proposition. The same basically holds for Joseph Smith’s editing here in Alma 5:45 for the 1837 edition. Originally, the text read “do ye suppose that I know not of these things myself”, which is readily understandable; even so, Joseph decided to attach the not to the preceding verb suppose, perhaps because it seemed more natural to him (“do ye not suppose that I know of these things myself”). Elsewhere the text has examples of not in either position for yes-no questions:
In none of these examples has the position of the not been changed. The critical text will restore the original placement of the not in Alma 5:45: “do ye suppose that I know not of these things myself ”.
For further discussion of the placement of not with respect to verbs like suppose and believe, see pages 1033–1035 in Randolph Quirk, Sidney Greenbaum, Geoffrey Leech, and Jan Svartvik, A Comprehensive Grammar of the English Language (London: Longman, 1985); also see pages 838–842 in Rodney Huddleston and Geoffrey K. Pullum, The Cambridge Grammar of the English Language (Cambridge: Cambridge University Press, 2002).
Summary: Restore the original placement of the not in Alma 5:45 (namely, in the clause following the verb suppose: “do ye suppose that I know not of these things myself”).