You Must Submit Separate DS-160 Applications
In general, when applying for a US visa, each traveller must submit a separate DS-160 application form. In your case, you are applying from different countries, which means that you will attend interviews in different countries, so it makes sense to fill in separate applications.
Companions or Not?
You state you are flying in from separate countries. This indicates that you are not really travelling together. However, what really matters is whether or not you go through immigration checks together.
Will you be meeting your spouse after the immigration checks, once you are officially on US soil? If so, you are not travel companions.
Will you be going through US immigration together? If yes then you are travel companions and should add this information in your application forms.