There are different approaches:

If your subs have a highpass filter, connect your main outs to the subs, and then the hpf output on the subs to your tops. This way your tops don't get the low frequency stuff.

Another approach is aux fed subs, where you feed the subs from an aux bus, and then make sure that instruments with low freq content are put onto the aux bus. Tops are fed from your main outs as normal.

Yet another approach is to use an external crossover. Main outs to crossover. The crossover passes low freq content to the subs and the rest to the tops.