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) is PTFE and the butyl rubber component is usually white or clear.
If both the butyl rubber and the PTFE are 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 butyl rubber is facing the table. It is not a good idea to use that septa in HPLC or GC after the test.