I'm also writing on T.S Eliot's poetry for Mod B.
Generally I like to talk about 2 separate poems max per paragraph (otherwise it often gets confusing for the reader). If you're doing 3 paragraphs (like I usually do) you can either talk about poems A and B for each paragraph, or A&B for the first, B&C for the second and A&C for the third. I find the second approach works better for me.
You can start of with analysis of one poem, then bring the second one in by comparing its treatment of the same concept or theme, or how it creates the same/different effect.
E.g. For a paragraph on the concept of isolation in both Preludes and The Lovesong of J. Alfred Prufrock - 'This theme of alienation and neglect is similarly explored in 'Preludes', through desolate urban imagery ....' or 'Eliot also employs sensory imagery to portray the isolating effect of urbanisation in 'Preludes', as seen through....' etc.
If the topic or theme is explored differently, you could start it off with - 'Contrastingly, the concept of alienation is investigated in 'Preludes' through ...'
Throughout analysis of the second poem you can also occasionally refer back to the first - '.... contrasting against/mirroring that of 'Lovesong of J. Alfred Prufrock'.
Good luck, hope this helps