Hi, yes you can do both.
Autoencoders can be done using a specific network structure (specified in the config file) when one of the middle hidden layers has few outputs of size 1x1
By transfer learning, I guess you mean using pre-trained net weights. The network weights are saved in the 'net' variable returned from 'Train'
You can re-use this variable to train on new data.
Hope it helps,
Hagay