Not sure if you already have set up your keyboards in the external devices tab under options (there is no 49es in the list so just add one by selecting new keyboard). Make sure "receive from" pull down box is set to your keyboard, all MIDI channels 1-16 are highlighted and the split channels box is checked.
Then goto the 2 track headers, one for each instrument plugin and expand them vertically. The 2nd pull down in the headers is the instrument input and instrument (midi) channel. Set your 49se to midi channel 1 on one track and MIDI channel 2 for your S88MK2 on the other track. Then set keyboard midi channels to 1 for your 49es and 2 for your S88MK2. The 49es should be set to midi ch 1 by default at pwr on, but you need to change it to 2 physically on your S88MK2
