After setting up and Exchange 2013 SP1 server on Server 2012 R2 I ran into this small issue with a customer. Even though I had all of the send/receive connectors in the ECP set at 100M, I was still hitting the default 10M attachment size limits.
Here's how to fix that by changing the Global Transport Settings: (short answer)
Check to see what the size limits currently are -
Get-TransportConfig | ft MaxSendSize, MaxReceiveSize
Once you know those sizes then here's the command to change them to what you need -
Set-TransportConfig –MaxSendSize 100MB –MaxReceiveSize 100MB
I know these sizes are a little large but just using them as an example. Go ahead and bounce the Transport service just to be sure the settings take effect and you'll be good to go.
All of the other size limits can be set using the ECP under Mailflow and then Send Connectors and Receive Connectors.
Update: I've just completed reading almost all of Mastering Microsoft Exchange Server 2013
. This is an excellent read that will give you tons of insight into installing, maintaining, and mastering all there is to Exchange 2013. I highly recommend you give the book a read.