This answer will initially concern itself with your mini-question. Namely, "would rain clouds float in helium layer or only oxygen layer?"
It is doubtful if rain clouds would float in the helium layer. Firstly, due to the low density of the helium rain clouds will be denser and heavier, if they formed there, and so sink to lower altitudes. Secondly, the helium layer seems to be too high for rain clouds to be supported. Remember rain clouds mainly form and float in the troposphere which is a lower part of the atmosphere. The description of this atmosphere suggests the helium layer is above its troposphere.
The troposphere is the lowest layer of Earth's atmosphere. The
troposphere starts at Earth's surface and goes up to a height of 7 to
20 km (4 to 12 miles, or 23,000 to 65,000 feet) above sea level. Most
of the mass (about 75-80%) of the atmosphere is in the troposphere.
Almost all weather occurs within this layer. Air is warmest at the
bottom of the troposphere near ground level. Higher up it gets colder.
Air pressure and the density of the air are also less at high
altitudes. The layer above the troposphere is called the stratosphere.
Nearly all of the water vapor and dust particles in the atmosphere are
in the troposphere. That is why most clouds are found in this lowest
layer, too. The bottom of the troposphere, right next to the surface
of Earth, is called the "boundary layer". In places where Earth's
surface is "bumpy" (mountains, forests) winds in the boundary layer
are all jumbled up. In smooth places (over water or ice) the winds are
smoother. The winds above the boundary layer aren't affected by the
The structure of the atmosphere of this planet is unusual. On Earth a gas like helium would be found mainly in the thermosphere and, possibly, in the exosphere.
The thermosphere is located above the mesosphere. The temperature in
the thermosphere generally increases with altitude reaching 600 to
3000 F (600-2000 K) depending on solar activity. This increase in
temperature is due to the absorption of intense solar radiation by the
limited amount of remaining molecular oxygen. At this extreme altitude
gas molecules are widely separated. Above 60 miles (100 km) from
Earth's surface the chemical composition of air becomes strongly
dependent on altitude and the atmosphere becomes enriched with lighter
gases (atomic oxygen, helium and hydrogen). Also at 60 miles (100 km)
altitude, Earth's atmosphere becomes too thin to support aircraft and
vehicles need to travel at orbital velocities to stay aloft. This
demarcation between aeronautics and astronautics is known as the
Karman Line. Above about 100 miles (160 km) altitude the major
atmospheric component becomes atomic oxygen. At very high altitudes,
the residual gases begin to stratify according to molecular mass,
because of gravitational separation.
Presumably the planet formed in unusual circumstances, in terms of planetary science, and may have acquired its excess helium in a rare type of incident. Perhaps a nearby gas giant planet shed large amounts of its helium atmosphere and this was captured by your planet.
If lighter-than-air balloons or airships were going to stay aloft using open canopies, they have to somehow rise high into the helium layer before descending to capture enough helium to remain buoyant and airborne. This suggests that a balloon or airship would have to be launched upwards with a not unreasonable velocity to reach high enough for the helium capture to take place. This could be accomplished with a giant catapult or rocket propulsion.
However, it would be unfortunate if an airship or balloon failed to get enough helium and plummeted planet-surfacewards. Let alone being hurled high into the upper atmosphere before their perilous descent. Aviators both passengers and crew, will need breathing apparatus because it is likely there will be insufficient oxygen in the helium layer to sustain life.
It would be an ingenuous exercise to construct a model of this planet and its formation to explain how it acquired such a considerable layer of helium as part of its atmosphere.
In summary: open-canopy balloons and airships seem dubious at best. Methods for attaining altitudes necessary to collect enough helium appear to be too dangerous to be fit for the purpose. rain clouds are unlikely to float in the helium layer, and will be found in its oxygen-nitrogen layers in its troposphere.