Hey Juliana,
Yes you can include a imaginary part of the index of refraction of your profile materials. When the mode solver finds the modes it will give the complex effective index which can be converted to a loss or dB/km.
When setting the width in the Profile Manager you are setting the default waveguide parameters, so it will not change the profiles already placed in your project. Any new waveguide using that profile will reflect the different width. Instead double clicking the feature and changing the width directly will change the width immediately.
Regards