I may be a bit rusty with scheme but I think something like this would work for you,
(define (number->second-pair n)
(cons (inexact->exact (floor n))
(inexact->exact (floor (* 1000000 (- n (floor n)))))))
(number->second-pair 5.1234)
returns (5 . 123400)
(number->second-pair 1)
returns (1 . 0)