The master cylinder for the clutch should be next to the brake booster.
The clutch fluid reservoir, master cylinder, slave cylinder and fluid lines are pre-filled with fluid at the factory during assembly operations.
The hydraulic system should not require additional fluid under normal circumstances. The reservoir fluid level will actually increase as normal clutch wear occurs. Avoid overfilling, or removing fluid from the reservoir.
Clutch fluid level is checked at the master cylinder reservoir. An indicator ring is provided on the outside of the reservoir. With the cap and diaphragm removed, fluid level should not be above indicator ring.
To avoid contaminating the hydraulic fluid during inspection, wipe reservoir and cover clean before removing the cap.
I seriously don't think that a low fluid would have anything to do with a noisy gear train.. Try changing the fluid in your trans first.