I am not sure why you would need another table to store Employee Id numbers. You can include everything in one table and you can use IDENTITY (Property)
] to auto generate the EId column. Here is a sample of how your table would look.
CREATE TABLE EmpRegister
EId INT IDENTITY(1,1) CONSTRAINT PK_EmpRegister PRIMARY KEY,
When User enters the Employee Id you can check if it exists or not like this
SELECT COUNT(*) FROM EmpRegister WHERE EmployeeId = 'Value entered by user'
If the EmployeeId entered by user already exists the count will return a non zero value else it will return 0.