Suppose we want the variable t[i] to be equal to the ceiling of a variable x[i]. The ceiling function is indeed not implemented in Couenne, but it suffices to declare t[i] as integer and then add the two constraints
eps + t[i] >= x[i]
eps + t[i] - 1 <= x[i]
where eps is a small-enough constant, say 1e-5. A nonzero eps allows for unicity of t[i] (in case x[i] is itself integer), although x[i] 3.000009 will result in t[i] = 3. There are simpler implementations in case you only require t[i] >= ceil (x[i]) or t[i] <= ceil (x[i]).
Hope this helps,
Pietro