The non-deductible federal taxes was prefilled all under my name and nothing under my husband. Do I leave that or prorate between my husband and myself?

If you have joint LLC with your husband, you have to prorate all income and expenses, including taxes. Otherwise, you might leave in as is. 

No Joint LLC - we have our own separate W-2's from different employers

If it is about W-2 income, then amount of Federal tax should be entered exactly like it is in your W-2(s). Please adjust the amounts manually.