analysis a knee structure

for my final year project I have to analysis the stresses in the knee, with that i have created 3 separate STL file for the cartilages and the meniscus. and I have a dew questions:

1) when i import the model should I import them separately as sat file --> create assembly instances or import them as an entire combined model? 

2) how do i select surfaces of the part when setting BC and applying load