The PTFE (Teflon) part of the septa faces the sample (i.e. faces toward the vial when placed on the cap).
If you have any doubt if the septa is inserted into the cap properly, the rule of thumb is that the colored (often red) and the silicone rubber component is usually white or clear.
If both the silicone rubber and the PTFE is clear, and the septa is out of the cap, a simple test is to put the septa on a smooth table top. With your forefinger, try to slide the septa on the table top. If it slides easily, the PTFE is facing the table. If the septa does not slide easily, the rubber is facing the table. Probably not a good idea to use that septa in HPLC or GC after the test.