I recently began running a protien based mixture through an HPLC, using .1% TFA as the main eluent, but found that multiple peaks were coming off about the same time. Are there any suggestions on what eluents or type of gradient that I can use to better separate the peaks???

there are many possibilities (assuming you are doing reversed-phase):
1. you can manipulate the gradient; longer gradients give more resolution
2. you can manipulate the pH, either by playing with the TFA concentration or by using a TFA buffer system
3. for drastic changes in the chromatography, you can use different organic solvents: IPA, MeOH, MeCN
There are a few other things worth doing, but this is a good start.