for the second question,  yes pytorch can work with 16 channels.
for the third question;
read 16 grayscale image and concatenate them and convert tensor.  if your image size is 512 x 512. your concatenated input size 16 x 512 x 512.
u can write custom dataset class for reading images and make them 16 channels input.
Check the link 30 for writing custom dataset.