Hi Petyr- Custom objects behave similar to opportunities in marketo. There will be a trigger and a couple filters, e.g. Has [Name of Custom Object]. So if you custom object is called "Product", make a smart list and look for the "Has Product" filter.
You can see fields on a custom object in the constraints of the trigger and filters available with that custom object. When you select a constraint the data from those fields will be available to use in a smart list.
Note that you can't see the fields as columns in a list view and if you need to use the data from a custom object in an email you'll need to use email scripting (this is because one person could have multiple entries on a custom object.)
aside de from filtering them, you do not really see them. Vote here: Make it possible for CRM (SFDC/MS Dynamics) custom objects to show up in the custom object tab in the Lead detail screen