Just to expand on Manuel's excellent answer a bit more.
How do I set up the limits of integration for this problem?
The support is $\{(x,y): 0\leq y\leq x\leq 1\}$.
The exterior integral, which we choose to take over the supported distribution of $Y$, must "run over the entire gauntlet": the interval, from the infimum to the supremum, for $Y$. So we integrate respective to $y$ from $0$ to $1$.
$\def\E{\operatorname{\mathsf E}} \begin{align} \E(XY) & = \E(Y\E(X\mid Y)) \\ & = \int_0^1 y\,\mathsf E(X\mid Y=y)\,f_Y(y)\operatorname d y\end{align}$
The interior integral, which is over the support of $X$ when given a $Y$ value, must have its bounds set relative to that value. So we integrate respective to $x$ from $y$ to $1$.
$\begin{align}\E(XY) & = \int_0^1\int_y^1 xy\,f_{X\mid Y}(x\mid y)\,f_Y(y)\operatorname d x\operatorname d y \\[1ex] &= \int_0^1\int_y^1 xy\,f_{X,Y}(x,y)\operatorname d x\operatorname d y \\[1ex] &= \int_0^1\int_y^1 12xy^3\operatorname d x\operatorname d y\end{align}$
Of course, there is nothing stopping us from doing it in a different order. Fubini's Theorem states this should be the same, if the expectation of the absolute value is finite .
$\begin{align}\E(XY) & = \E(\E(XY\mid X)) \\[1ex] &= \int_0^1\int_0^x xy\,f_{X,Y}(x,y)\operatorname d y\operatorname d x \\[1ex] &= \int_0^1\int_0^x 12xy^3\operatorname d y\operatorname d x\end{align}$
Choose whichever path is easier to pass through.