It depends on what the decomposition is. It is more complicated to describe than do. Let me recap a bit:
Effectively you decompose T into two smaller sets U and V such that you know the fund. grps of U and V and UnV. Obviously, any loop in UnV defines a loop in U and a loop in V.
Then the fund grp of T is the (free) product of the fundamental groups of U and V modulo the relations imposed by the fact that loops in the overlap are identified.
Those relations are the "modulo N" part.
I guess this isn't a direct answer, but then I wouldn't calculate N, i'd describe explicitly the relations on the overlap, that implicitly tell you what N is.
Let's do an example where we already know the answer: the torus.
Let U be the torus less one point - the punctured torus.
Let V be a disc around that puncture point.
U can then be deformation retracted to the bouquet of two circles, thus its fundamental group is the free group on two generators F_2. Let the gens be g and h, we'll explain why in a second.
V has trivial fundamental group
UnV is homotopic to a circle. It's fundamental group is Z; let t be some (homotopy class of) loop generating this group. In V this is sent to the identity, as V is contractible. In U this loop is sent to the path ghg^{-1}h^{-1}. To see this, imagine the torus as the square with opposite sides identified. U is then this square with, the centre missing, thus the punctred torus retracts to the boundary of the square, which identifies to give two circles joined at a point. A loop around the hole retracts to be a path that goes along the top edge of the square, down the side along the bottom and up the other side again, right? So it is a path around one circle, then around the other, back along the first circle in the opposite direction, and then along the second circle, again in the opp. direction, ie ghg^{-1}h^{-1} in the fundamental group.
Phew, this is complicated to write, but draw a diagram to see what's going on.
Anyway, by the van Kampen Theorem, the fundamental group is
(F_2)*(e) = F_2 modulo the relation that ghg^{-1}h^{-1}=e; we identify those loops we described.
This means that we make gh=hg, ie abelianize F_2=ZxZ, so N in this case would be the commutator subgroup of F_2.
It sounds more complicated than it is, honest.
N is the subgroup generated by the relations we impose because of the overlap.