Im new to the LiPo batteries and I bought a Protek prodigy 65 ac charger and a protek 5000mah 2s 35c lipo. I read through the instructions a couple times but still cant figure out whats the best way to charge the battery. I am able to balance charge it but at what amps, how long do I set the safety timer, and the capacity shut off? Also with the storage mode have no idea what to put the settings at

No reason to use the capacity or timer safety functions, just turn them off

Charge the pack at 5 amps

Whenever your packs are not in use they should be kept at storage voltage (50% or 3.85v / cell)

Cheers

and when I put them on the charger in storage mode would I set that at 5 amps as well?

Not familiar with your charger

Some will only charge up to storage voltage from empty

Some will only discharge down to storage voltage

Some will either charge or discharge depending on the starting voltage of the pack

If charging up use your normal charge rate

If discharging you will more than likely be limited by the discharge power of your charger, regardless of what rate you enter

Most have very small discharge current rate limits (5 - 30 watts)

Check the spec sheets for your charger and it will tell you what the discharge limit is

Simply divide it by the pack voltage and you will work out the max discharge current

Example
20 watt discharge limit
3s pack

20w / 12.6v = 1.58 amps max discharge current

Cheers

+ on Crusey's posts.

the charger is capable of charging or discharging in storage charge mode depending on the voltage when connected. Here are the specs i got off a main.
Specifications:
Input Voltage: AC 110V-240V, DC 11V-18V
Charge Current: 0.1-5A, 0.1A step
Discharge Current: 0.1-1A, 0.1A step
Power Supply Output: 5A
NiCd/NiMH Cells: 1-15 Cell
LiPo/Li-ion/LiFe Cells: 1-6 Cell
Lead-acid (Pb): 2-20V
Temperature Sensor Port: Yes
USB Port: Yes
Balance: 2-6 Lithium Cells
Case: aluminum
Display: 16x2 character LCD
Dimension: 135x125x34mm

the instructions dont give much info.

If it has a discharge limit of 1 amp then use that

A 1 amp discharge of a 5000mah sized pack will take 150 minutes to take it down from full to storage voltage

A lot easier to run the pack in your car down to your LVC cuts in

Throw it back on the charger and charge it at 5 amps before storing

Charging at 5 amps will take 30 mins from empty to get to storage voltage

Cheers

Pg 19 of your manual says this charger is set to discharge or charge a lipo to storage conditions as dictated by the voltage when you connect it.

Due to limited discharge wattage (5watts), it will be faster to take care of any needed discharging in your RC unless the voltage is pretty close to storage value. I make sure mine are charged to storage since that's faster.