For your first question you've asked, you need to get the binding (and cast it to JControlListBinding) of the selectManyCheckbox from the bindings and set its selected values via setSelectedIndices method.
If you want them all to be preselected, you can iterate through all values, find their indexes, put them in an array and then pass as a parameter to the setSelectedIndices method.
For the second one,
I have no idea about the reason behind such an operation, but i guess you could create an appropiate Row with the value the has been typed in to the box, then you could add it to the RowSet (via createRow() method of the ViewObjectImpl.) that is bound the selectManyCheckbox.
Maybe because of my rookieness, I don't think that the questions you've asked can considered to be basic. :)
Bonne chance in your ADF adventure by the way.