Let's not forget, just like in real life football, the teams with the most money, facilities and assets(in Top Eleven case: rests, treatments and morale boosters) have a better chance of signing better players and have an overall better quality team. However, again just like in real life, we all have the opportunity to adjust our strategy and try to outfox our opponents, regardless of their team quality and how much money they spend. You might not always win, and during my 8 years of playing this game, I've had some dry spells in which I lost many matches in a row, even though I always had my team between 90-100% of my level. I used to try a "one formation fits all scenarios", which sometimes might help in the short run, but I've found out that rotating your players, having different strategies and training your players helps a lot.
1000 tokens sounds to me like a lot, I personally never had more that 250 at any given time. I rarely buy scout players, I like to focus on power training youngsters, so most of my tokens are spent on rests, treatments and morale boosters. Sort of like an Ajax mentality.
All I can say is try not to get too discouraged by big spending managers, try to outsmart them and have fun!