In a one-to-one relationship, where should the foreign key be placed?
It is acceptable to have mutually exclusive attributes in a table.  If you only have one pair of such attributes, this may be the most practical solution.

However, some people may look at your situation as a sub-typing issue.  In this view, you are missing the superset entity.  You have a collection of (something), some of which are employees and some of which are customers and some of which are also users.  

Have you also considered what happens if an employee also happens to be a customer?  Is that important to your system or is that something that would be considered coincidental?

If you think its important to treat all users as a feature of one type of thing, then you need to implement the (something) which is currently missing from your table definitions.

Consider the following ERD:



If you supply the missing superset entity, then every employee is one of these, as is every customer, and also therefore every user.  The hard part of this is coming up with a reasonable name for this superset, but it solves the issue of having to figure out which foreign key to follow from user.  It also makes a connection between employee and customer should one happen to exist, and should that connection be of interest.