Just make sure that strainer cant p/u any large particle which can jam the impeller . Trays can be left in it, but its up to you. Is ithis FOWLR or reef?
In case tank can not sustain clarity, then you can decide to add whatever media.

i just thought wont my water be really dirtycause i have no skimmer?

so take out the the dividers out as well so its just water in the filter?

At least it wont produce!

so i if run it empty would if reduce nitrates?

Since you say you have enough LR and LS, why not run empty as return pump (no media, more water it pump). You can always add media when need to.
I have run successful Reef tanks (long but shallow) using nothing but Protein skimmer, Powerheads, and specific flu bulbs (high tech such as MH was too expensive and prior to PC)

hey i have plenty of live rock and a 4 inch sand bed ......and i just have corase media in my canister filter.

should i keep the media or just run the filter empty?