When this unit enters play, each player takes 2 indirect damage. is there possible to inflict all the 2 damage to an unit that has less than 2 hit points, and by so avoid 2 damage full hit for some other targets ?

No, you can not assign more indirect damage to a unit or a capital section that are needed to destoyed theim.

For example if you have a unit with 3 HP and thougness 2 you can assign a maximum of 5 damage to this unit.

Please see the FAQ you have the answer of nearby each of your question :-).