some inbuilt amp filters you can bypass (turn off). this way only the outboard xover takes effect.
if this is not possible, you can still effectively not use them. for example, if you wish to HP some splits at 100Hz:
*set the outboard xover to 100Hz
*all frequencies above ~100Hz remain full level and things are filtered off below this
*set the amp xover to much lower than 100Hz, say 40Hz: it will have no significant effect
likewise, if you wish to LP say at 80Hz:
*set outboard xover to 80Hz
*set amp xover to 200Hz: has nothing to filter really, so has no significant effect
as mentioned above, you can be tricky and 'cascade' or combine filters for a steeper one.
however, to create the smoothest filter, you want to set them exactly the same. this can be tricky on most xovers because the marking on the xover dials are never exact!
but, if it's pretty close, the effect is as good as you need.
so if you set
both the outboard xover and amp xovers to HP at 100Hz, the slope is additive. so if each is a gradual 12dB/oct slope, they cascade to a nice steep 24dB/oct slope. this may be better than 12dB/oct in many setups.