In general they can be very different. For example take the subscheme $Y$ of $\mathbb{A}^2$ given by the ideal $(x^2,y)$. Here the blow up is covered by the two open subsets
$$U = \mbox{Spec} k[x, y][t]/(y − x^2t),\qquad V = \mbox{Spec} k[x, y][s]/(ys − x^2)$$
In particular the blow up of $Y$ is singular, whereas the blow-up of $\mathbb{A}^2$ at a point is not.
In general, even if you assume that both blow-ups are smooth, all sorts of things can happen depending on how complicated the ideal sheaf is. For example the blow-ups can have a different number of exceptional divisors and not even be related by a finite map. Even worse, every birational morphism $X'\to X$ is the blow-up of $X$ along some ideal sheaf.
On the other hand I guess it is true is that there will be some third blow-up $Bl_{Z}(X)$, which dominates both $Bl_{Y}(X)$ and $Bl_{Y_{red}}(X)$.
Related to all this is also the concept of ideal closure. If $I\in O_X$ is an ideal sheaf, then the ideal closure of $I$ is the ideal sheaf $\overline{I}$ consisting of all elements $r\in O_X$ satisfying some integral equation $r^n+a_1r^{n-1}+\ldots+a_n=0$ with $a_i\in I^i$. See chapter 9.6 in Lazarsfeld's book. It is known that the blow-up of $X$ along $\overline{I}$ corresponds to just taking the normalization of the blow-up along $I$ so at least the two blow-ups are related by a finite surjective morphism and so in that sense you can relate blow-ups of ideal sheaves with equal ideal closures.