When building a CAML query using U2U CAML Query builder, if you need to search for a user then the only option is to provide user's login name. That's not neat and you can beat it by providing an extra parameter called "LookupId" with the field. For example
MyQuery.Query = "<Where><Eq><FieldRef Name='Employee' LookupId='TRUE' /><Value Type='User'>UserID</Value></Eq></Where>";
After specifying the attribute, you can select a user by his/her ID.