Q:

How to prevent battery drain when loaded?

I have a circuit consisting of 4 relays and 3 dc motors, with 4 diodes, resistors, and leds connected within. I have two 6 volts battery from the UPS. I need to obtain a negative voltage so I do workarounds with the two 6 volts battery so that the terminals are +6, GND, and -6 volts.
The problem is, the battery gets drained (or the voltage supply decreases to 2 volts) when the circuit is fully constructed. Proper output cannot be obtained. (By the way, each component of the circuit perfectly works well)
I am planning to have a separate voltage supply or battery for the relays and the dc motors. I wonder if this is the right thing to do.
What can you suggest?

A:

If you mean the (freshly charged) battery voltage sags when you power on your circuit, then it sounds like you are overloading the batteries (e.g. asking them to supply more current than they are capable of without significant voltage drop)  
You probably just need some bigger batteries (or fresh ones if the ones you are using are dead)
A separate supply doesn't seem necessary unless you want to e.g. run the motors from a different voltage or keep things isolated for other reasons. In any case, if you have mentioned everything in your circuit then what else is there to power apart from the relays and motors?
To confirm this, could you update your question with:

The current draw of your circuit in it's various states (e.g. motor off, motor on low/high speed, etc)
The model/datasheet for your batteries, or failing that what is printed on them. Also how old they are (or a rough estimate) 

Also a model/datasheet for the motors, and/or a schematic would probably help if you can manage it.

A:

I really don't recommend using batteries to supply separate positive and negative voltages.  The loading is not going to be equal, so they will drain and age at different rates.  Using batteries without a voltage regulator also means the supply voltages will change with time.  Some components really do not like this and may lose accuracy as the voltage fluctuates or falls out of the optimal voltage supply region.
Instead, use some larger or newer batteries since they are being loaded too much.  Then use a positive and negative voltage regulator with a charge pump to generate the negative voltage.  There are packages out there that provide all-in-one, or different groupings of the three functions.  This is only one general method.
Essentially, use a full DC-to-DC converter since you need negative voltages and are using batteries as your source.

