Does a 1999 Chevy Malibu have to be running check transmission fluid?

No, you do not have to have a 1999 Chevy Malibu running to check the transmission fluid. In fact, it's generally recommended to check it while the engine is running, but only after it's been warmed up to operating temperature. However, you can still get a reasonable assessment of the fluid level (though not necessarily the condition) with the engine off. The key is to find the dipstick (usually located near the engine, often with a different color handle than the engine oil dipstick) and check it according to your owner's manual instructions.