Trooper A has marksmanship level 2. Trooper A makes a BS attack against trooper B. During the attack, can model A choose to use marksmanship level 2, but not use marksmanship level 1?
Yes. You can choose to not use Marksmanship L1 if shooting at, for example, a Bolt. It is a distinct skill from Marksmanship L2, all relationship the level 2 has with level 1 is that it also give you the level 1. http://infinitythewiki.com/en/Special_Skills#Special_Skill_Levels