I'd do it pretty much exactly the same as a normal language analysis except I would juxtapose the varying approaches. Analyse the language in the exact same way, just work the second one in there in a "similarly," or "in contrast" basis. I was never taught specifically how to do one, I just was used to juxtaposing things from Legal Studies, so that's pretty much how I let my comparative analyses be and my teacher always like them...
To give you an idea of what I mean - I wrote a sample for some of the kids at my school on a comparative piece they had to do...*This is not intended as a 10/10 sample and can be significantly improved, it is just intended as a demonstration of one approach you could take to comparative analyses.
Following the recent abduction and subsequent murder of Melbourne woman Jill Meagher, there has been large-scale discussion concerning the implementation of closed-circuit television cameras (CCTV). In response to this, both Charlie Bezzina, a former homicide detective, and the editor generate pieces arguing for the immediate installation of CCTV around Melbourne City. In “CCTV: Do we need more? YES, it is simply one of the most vital tools for investigators”, (Herald Sun, 28/09/12), Bezzina contends that whilst CCTV will not actively prevent crime, it is still a vital factor in police investigation. Similarly, the editor argues that CCTV will both prevent and help solve crime in the editorial “Jill Meagher’s disappearances shows the need for greater CCTV coverage in Melbourne”, (Herald Sun, 28/09/12). The latter adopts an explanatory tone and style whilst Bezzina opts for an authoritative tone to complement his bullet-point style and structure. Such tones are aimed to target the wider population of Melbourne. Bezzina focuses heavily on the use of anecdotal evidence and confronting language, whereas the editor appeals directly to the readership’s sense of safety. Both article are accompanied by a grey scale photograph; the editor’s of Jill Meagher’s face and Bezzina’s of a CCTV camera portion.
Bezzina initiates his article by focusing on the abduction of Jill Meagher and the investigatory aftermath. In saying it is “so significant” that someone was speaking to Meagher prior to her abduction, he intends to instil a sense of relief in the audience that this vital piece of the case occurred. He compounds on this intended sense of relief in saying “We only know this because [of] CCTV”, aiming to capitalise relief into gratefulness of CCTV’s presence. The author structures this beginning in a ‘bullet-point’ fashion, using short, sharp sentences beginning with ‘it’ three times in succession. In creating such a mental list of arguments for the reader, the flow of the article is disrupted with the concession “In some ways I have to agree”. Such a statement is intended to surprise the reader and garner their interest, positioning them to be more receptive to Bezzina’s future arguments whilst lending him the credibility of an unbiased man. This is in stark contrast to the editor’s initial language; the editor immediately begins informing the reader, utilising loaded language consistently throughout her opening information. In situating phrases such as “sudden breakthrough” and “baffling case” in close proximity to each other, the editor aims to ingratiate CCTV for the Melbourne population; in positioning the case as “baffling” and thus connoting something unsolvable, CCTV is cast in a positive light as it enabled such an immediate solution. In this way, the editor aims to directly reinforce their contention in the eyes of the audience whereas Bezzina intends to make the audience more receptive to his future arguments.
So in the intro I just sort of meld them together and the paragraph is sort of split into one or the other. I was being slightly lazy because it was very late after midnight - you wouldn't have to do a sort of 50/50 paragraph, you could even go like line by line comparison and make it seem really seamless.
tl;dr use the structure you've been taught in a single analysis and just meld the other one in there.
In terms of what your teachers are telling you. You can do whatever you want. You're marked on the quality of your writing. I would group the arguments/way they use language in my paragraphs (or you could even do it chronologically and compare the language at the beg/mid/end of the pieces).
I've also heard recommended that you do five paragraphs; the first two on Article A, the first two on Article B, and then the fifth a comparative paragraph. Personally, I think that way is full of shit.
The most effective one is the one you're most comfortable with as a general rule. You'll find a whole bunch of people structuring it a whole different way. I personally prefer juxtaposing because it just gels in my head. Do whatever you please, the chances of you getting two articles to compare on the exam is smaller than a bigot's brain.