If you use the same file and login as last year and just change it to 'married filing separately' then the system should carry the losses over for you.
If you are having to start a new file in order to file separately this year then you will have to manually enter any data that would have carried over from prior years including any assets or losses. If you had passive losses you will enter them when entering your schedule E. If you had a Net Operating Loss then you may have to split that with your spouse depending on your state's community property rules. You can enter the NOL by typing NOL into the search bar and clicking 'jump to'.
@edSha