Assuming that John has neither been charged with assault nor is evading such charges: Can John sue for two separate counts of libel (one for claiming that he is charged with a crime and one for stating that he is evading criminal charges) or can he use for just one count of libel, based on following statement made about him: "John is at-large from assault charges"?
How many counts of libel for the false statement: “John is at-large from assault charges”?
John may plead his claim(s) either way, but the choice is largely inconsequential to the issue of recovery. There is no such thing of "x dollars per claim of defamatory falsehood", especially where the falsehoods are as intertwined as in the example you outline.
What matters is the extent to which a false statement tends to harm and/or provably harms the plaintiff's reputation. It would be futile to try breaking down that harm (whether actual or, in the case of defamation per se, the presumed damage) per each particular item that can be dissected from one same defamatory falsehood: the allegation of assault, of being charged, and of being at large.