Considering $H \in \mathbb{R}^{N \times N}$ a real symmetric matrix which has both positive and negative eigenvalues, and $B \in \mathbb{R}^{N \times M}$ a real matrix with positive entries.
Can I find a condition to make $ \operatorname{trace}(H) \ge \operatorname{trace}(B^{\top}HB)$?
Since $H $ is real and symmetric, it can be diagonalized as $H = V^T D V $ where $V^T = V^{-1} $ and $ D$ is diagonal. Thus your expression may be rewritten as
$ tr (D) \geq tr ( B^T H B ) = tr ( B B^T H ) $ where I have used that $tr (D) = tr (H) $ and the fact that the trace is invariant under cyclic permutations.
With this in mind, one obvious sufficient condition may be $B^{-1} = B^T $ in which case the equality holds.
Another example: pick $B $ such that $B B^T = H $ so $tr ( B B^T H) = tr ( H^2) = tr (D^2) $. So now you should pick $D $ such that $tr (D) \geq tr (D^2)$, for example, having positive numbers smaller than 1 in the diagonal.
I'm aware these are not general conditions, only particular cases... but I guess this way you can build more examples and maybe get something more general.