Multiple inputs for Dijkstra's algorithm
Does your requirement have a function through which the both matrices are related 
If yes then on the basis of that function find a new weight matrix. Use this matrix on the flow path
If no, then try running matrix one first and then two and vice-versa and choose the one with corresponding cost output to your requirement
The inputs to Dijkstra's algorithm are a directed and weighted graph, generally represented by an adjacency (distance) matrix and a start node.
I have two different distance matrices to be used as inputs, representing two different infrastructure (e.g., roads and cycle ways). Any ideas how modify Dijkstra's algorithm to be use these two inputs? I want to implement in Python. 
Thanks!