What kind of boundary conditions? It depends on the problem, PDE and conditions.

If you have Dirichlet boundary condition on a domain, simply use at the end of assembling.

If you have Neumann boundary condition, there are cases where it automatically imposed due to the nature of FEM.

If it is Robin boundary, you have to work with the discretization properly.

For more details of simple problems, you can refer, Kwon-Bang and understand

https://www.math.uci.edu/~chenlong/226/Ch3FEMCode.pdf

http://ieeexplore.ieee.org/document/6514772/