There are two options for you here. Either you can create a new family site for your spouse. Look for the "My Sites" drop down menu in the top-right corner of every MyHeritage page you are on and choose the 'Manage my family sites' option, there you will find a button to create a new site. This will create a completely new site for your spouse containing her family's tree and photos and feeds under your account.
The other option is to create a new tree under your family site. This can be done by going to the Family Tree tab> Manage Family Tree tab> Add tree.
It's entirely up to you to decide which option to choose.
If you have two sites at MyHeritage, they are unique and cannot be combined.
Just continue it, I don't think there is any way to merge them later(at least I havent found one). After the tree is completed or as you go along it will make a brach that signifies different familys merging.