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I have 2 battery source connected together... Positive to positive. Eg. 6V + connected to 3V +. How do I measure voltage on the 3V source? Do I need a diode in between?

you cannot connect two batteries together in parallel. if connect +6V to +3V and two negative together, 3V battery becomes a load of 6V battery.

Sorry, I mean I connect them in series. I wanted to see if the 6V can boost the voltage of the 3V, but how do I see the voltage of the 3V battery while in the connection?

add a voltage meter to the +/- of 3V battery.

I added a voltage meter to the 3V battery, but it don't measure the actual voltage of the battery.. it's taking the voltage from both side... 6V and 3V... Any solution? 6V charging 3V, how to measure the voltage of 3V while charging?

when two batteries in series, both batteries are outputting power, so 6V battery will not charge 3V battery. If you connected two batteries in parallel, higher voltage battery (6V) will charge low voltage battery (3V) with the current of (6-3)/R, so you need to add a charging resistor to low the charging current. e.g. if you want to charging current 1A, you will need R=(6V-3V)/1A = 3 ohms with power P=3V*1A = 3 Watts.

I,ve edited this circuit to show all metering and the load resistor to give a current path to charge the 3v battery so take a look at https://www.circuitlab.com/circuit/9tc2tnekmkmz/question/ to see it. The 100 ohm resistor can be changed to whatever is needed to get the current you want.

good design! when current is large, you need to consider the wattage of resistor.

Thanks for the compliment. The circuit was intended to get across to i-link the fact that there has to be a path for current to flow. It might be suitable for a lab level lash-up but not for a commercial design which would require knowledge of the batteries used and also would require much better control of the current than a simple resistor would provide.