The only reason I don't assign skill points right away is for better management of progress.

Either I assign after every 15 skill points, which is equivalent to 1 Quality point or for fast trainers, I accumulate until about 150-200 so it will give me time to decide on how I want to distribute the points i.e. decide on special ability (based on performance) or assign all to skills.

Any unassigned skill points, also affects the training progress. The game takes into consideration all the skill points accumulated. So regardless of if it is assigned or not, the progress will be impacted.

However, I am not sure if cup draws would take into consideration unassigned skill points. I don't really bother much about cups, so I don't take notice of this.