When using a lookup field as the merge field in a Soapbox Mailer email, you'll see that the merged value is the ID of the related object's record, rather than a more human-friendly value, like a first name. To change this behavior, do the following depending.
1) Determine which fields from the lookup object you'll want to merge (for instance, the FirstName value from a custom lookup to the Contact object from the Account object)
2) Create a new text formula field on the object you're using in your merge (for instance, if the lookup field you need is on the Account object, create a new text formula field on the Account object)
3) In the formula field's formula section, insert the proper field to lookup in the lookup object (for instance, if the lookup I want is the FirstName field on the Contact object that is looked up using the value entered for an Account object's PrimaryContact__c field, enter "PrimaryContact__r.FirstName" without the quotation marks")
4) Save the new field
5) Merge the new custom formula field you just created into your Soapbox Mailer email (for instance, if the field you made above is PrimaryContactFirstName__c, use the merge field {!Account.PrimaryContactFirstName__c}
6) Celebrate!
Happy emailing!