I think you are getting confused due to the naming convention you are using. For T you can use any symbol to represent the function W in T. It is perhaps best not to use the symbol W in T's definition because it is confusing you. Try using f instead.
ClearAll[T, W];
W[L_, r_] := 1 + 3 L + 2 L^2 - 6 r*L - 6 L (r*L) + 6 (r*L)^2
T[L_, r_, d_, koff_, u_, f_] := ((u/d^2)*f[L, r] + 6 u (L - 1)) + koff (u/d^2) f[L, r]
There I have used f the symbol that takes the function. Now, when I call the function with W all works as expected and it is clear what W is and what f is.
T[L, r, d, koff, u, W]
(* 6*(-1 + L)*u + ((1 + 3*L + 2*L^2 - 6*L*r - 6*L^2*r + 6*L^2*r^2)*u)/d^2 +
(koff*(1 + 3*L + 2*L^2 - 6*L*r - 6*L^2*r + 6*L^2*r^2)*u)/d^2 *)
$$\frac{\text{koff} u \left(6 L^2 r^2-6 L^2 r+2 L^2-6 L r+3 L+1\right)}{d^2}+\frac{u \left(6 L^2 r^2-6 L^2 r+2 L^2-6 L r+3 L+1\right)}{d^2}+6 (L-1) u$$
Also, a point to note is that you should not create symbols that start with capital letters in your notebooks. These may clash with current or future symbols that Wolfram adds to the language. For example, consider N or E.
Hope this helps.
Win the definition ofT. Just writeT[L_, r_, d_, koff_, u_] := ...– eldo Nov 10 '15 at 16:28Win the definition ofT. – Mary Nov 10 '15 at 16:41