Neilson’s comments follow their 1-0 friendly defeat to Hamilton at New Douglas Park on Wednesday when Grant Gillespie headed a last-minute winner.
The 34-year-old former Hearts player was appointed to his new role at the end of last season but says things are moving in the right direction.
He said: “We’re getting there slowly but surely. They’re starting to implement the things I want them to do.
“But it was all about work rate here and trying to pass the ball. They took some risks here and there, and they made some mistakes.
“But you have to let them make mistakes at this stage of the season so they understand what they can and can’t do.
“Overall, it was a good exercise for us. It was pleasing. The boys were a bit fatigued going into the game because they had had a heavy day on the training ground as we try to build their fitness.”
Regarding new signing Prince Bauben, Neilson said: “He needs to prove his fitness because the ability is there.”
As for the match, Hearts youngster Jamie Walker struck the bar with a fierce shot from just outside the box before half-time.
And as the seconds ticked away, Danny Galbraith’s chip in to the box was met by Gillespie whose looping header just inside the post was out of reach of the diving Hearts keeper.