off top of my head, prestige is determined by:
W/L record (I think there is a mild bump for winning record)
Post season success in NT and PI, as well as going to post season often
Conference championships and Conference tourney championships
In D1 - I think lots of players getting drafted helps
I haven't kept track of typical improvements in one season. I would guess 1 letter grade is very good, often 1/2 letter grade will happen. You could look at successful teams under the history tab and get an idea of the progression.
I think a new player can expect a few seasons (4-6) to be to B+ prestige, if starting at C-... it really depends on how quick you learn the game. It took me awhile with my first D3 team to learn and understand things.... but after I learned some things I was able to grow D3 programs to respectable level pretty quickly (3-4 seasons).
Prestige, at the D3 level, helps with getting first dibs on recruits. higher prestige teams will have more players listed on their D3 board, and as D2 players drop down they will hear about it first. Once a battle is engaged - prestige does not matter at D2 and D3 from what I gather. At D3 the determining factor in winning battles is often how much $$ each school has (which you can figure out) and distance from the recruit. Prestige often gives the best schools a head start on players, but it may not matter if the player is closer to the lower prestige school. (recruits >360 miles away are significantly more costly to do home visits, etc.).
At D1 it is very important. For instance, an A+ prestige school at D1 may only have to expend 1/2 the effort on a recruit to win the battle vs. a C+ school....