In Internet Model there are four layers: Link -> Networking -> Transport -> Application.
I don\'t really know the difference between networking layer and transport layer
Cthulhu's explanation is ok but in order to understand a bit better, I recommend that you should read on the OSI Model
Transport layer handles port numbers, TCP, UDP, layer 4 PDU's and it's the first step in encapsulating and segmenting data in order to send it across the network
PDU = protocol data unit , it's a piece of information containing a header, the data segment and maybe a footer (see layer 2 encapsulation)
Network handles ip routing and delivery of data packets across the network
Each layer (regardless if it's OSI model or TCP/IP model with 4 layers) , each layer interacts with it's adjacent layer and provides an abstract framework for today's telecom purposes
Regarding your questions :
1). Flow control is a TCP mechanism for handling the size of the packet in order to prevent packet loss and retransmision, congestion control is another thing. Network layer doesn't decide anything, it simply tries to send your package over a network, if it fails, it will notify the upper layer about this problem and then the application or user should decide what to do).
2). TCP enables a 3way handshake mechanism to start a session, afterwards each packet is market with a counter and the receiver acknowledges receipt of senders package. In case he doesn't acknowledge, TCP resends that lost package. Networking layer will only forward packets and won't make any decisions regarding traffic control or packet ordering.
Further details are available in CCNA1 documentation or on the web.