If you marked yourself as married, the software will prompt another question if you want to file the returns together?. If you answer yes and finish the profile, you will not be able to remove his return and file a separate return.
However, you can finish both profiles, and on the payments page, file your return only.
If you are filing a separate return as married, you will have to report your husband's net income so the software can determine the eligibility for federal and provincial credits and benefits.
I hope this was helpful