{username:\'me\', companies:{\"yourcompany\":{...}}
I want to insert a company into a user record (user collection), to make:
{username:\'me\', companies:{ \
You'd have to build up your $set modifier programmatically:
var modifier = { $set: {} };
modifier.$set['companies.' + companyid] = { desksmemberships:[] };
And then use modifier as the third parameter in your findAndModify call.
You may also want to consider changing companies to be an array instead of an embedded object.
Node.js 4.x Update
You can now use the computed property syntax to do this directly in the object literal:
collection('users').findAndModify(
{username: usern},
[['_id', 'asc']],
{$set:{['companies.' + companyid]: { desksmemberships:[] }}},
{new: true},
function(){...});