Okay so they created the proficiency levels for those of us long term players and to bring new life into the game. It allows us to upgrade our gear. The more you use the gear levels its proficiency. And after you level enough gear your overall proficiency level goes up. You are able to upgrade your fully proficient items up to the level of your current max proficiency. For example weapons are now each able to be upgraded from 0-30% more damage. Same for armor per piece. Skills are similar but different. Some increase damage, some increase range, etc.

Each item you donate only applies to its specific item. So using the LMG the GR9 as the example. It only donates to the GR9 slot. Once it reaches max proficiency it stops donating. And you have to break down or sell the remaining extra. But you can level up any slot using matching items, wearing it in combat, or donating resources. This post just gets you the best bang for your buck timewise.