Is this is a spray fluxer prior to a wave soldering system or you are spraying flux for some other reason such as flip chip bump soldering?

Anyway as you know measuring flux thickness is not easy. You can use very simple wet thickness gauges if you are trying to measure thick films, say 50 microns and above.

If you are not familiar with this type of gauge, its very much like a comb with different length teeth. You drag the gauge through the flux and see which teeth make contact.

Now if you want the ultimatesolution there is an LED /Laser based system on the market from lumetrics that can measure wet film thickness in a fraction of a second and can do this in real time.

The best way to verify the spray patern is to use thermo paper on the bottom of the PCB.

You can also use it on the top to verify the hole filling.

A more accurate way is to get a template supplied from several thermo profiler vendors. The plate has holes in different diameter across the board.

The fax paper is on the top of the plate and give good image of the fluxer performance.

There are a few methods that are good rules of thumb for uniformity. You really should be looking at three points with regard to your fluxing. I will assume your question is related to a no-clean based process.

1) Uniformity bottomside surface.

2) Penetration of the flux into the through hole barrel.

3) Correct amount of solids being applied.

1) Uniformity of bottomside flux. (Meaning correct overlap of spray)

Visual method, this simple and easy test helps in determining general uniformity of spray pattern to the bottom of an assembly. To simplify you can use thermal fax paper to place an imprint of your spray pattern.

There are tools out there such as the ECD Flux-o-Meter that can also assist in both bottomside uniformity and topside penetration. Either way, this should be looked at as a simple no-quantitative test. If alcohol based flux is being used you can get a good image imprint by using thermal fax paper.

You can obtain these rolls of fax paper at Staples. If using a VOC Free type you will need pH paper (this too can be obtained by ECD and other sources).
For bottomside uniformity attache proper paper thermal sensitive side facing down to a sub-straight or surface the same size as the assembly in question.

Run the panel in the conveyor over the fluxer under normal conditions. Remove the panel prior to entering preheat. Allow the paper to dry and observe the patten. Adjust as needed to achieve a consistent pattern on the bottom of the assembly.

2) Penetration of flux through the barrel. Similar to the above. either use the flux-o-meter or purchase two sheets of bread board material from radio shack. This is just PCB materiel with equal holes drilled across the entire surface and plated.

Purchase at least two or three to simulate different pcb thickness. With this test, place the paper on the top or the PCB. Tape it down in place to insure the paper stays flat and is not lifted off the panel by the spraying of the flux.

(Note: you can also sandwich the paper between boards) Run the panel through the fluxer, again remove from the system allow to dry and inspect. You should see clear imprints of the holes in the panel, If not adjust as needed.

3) Solids remaining. This is perhaps the most important test. You can and should go to flux suppliers websites like Alpha Metals and Kester, Aim, Indium and so on, that will have these methods documented.

Simply, you want to confirm that the micrograms per square inch of flux on the surface of the assembly are correct and within specification for the flux. Typically, these number range from 900 micro grams to 2000 micro grams. Methods vary by supplier so I would suggest you contact the supplier of your given flux in use.

Most likely, you will need bare boards and an accurate scale with the ability of reading 4 or 5 digits in the gram mode. Check with your suppliers to insure your using their method of weight (wet or dry).