for MFS you need to create two separate returns in separate accounts. doing a second return in an online account will permanently overwrite the first return. your other option is a desktop version (full PC or MAC - 64 bit operating system) which allows the preparation of an unlimited number of returns so you can do two separate and a joint to see what's better.
with separate returns some credits are lost. generally a joint return produces the lowest total tax.
with MFS both must use either the standard deduction or itemized deduction.