TOC is particulate C and DOC. To find DOC, the sample must be filtered. In unfiltered water, you will only be able to measure TOC. I assume that there is not so much particulate C that it interferes with the analysis. Glass fiber filter is probably best to avoid DOC from the filter. Alternatively, you can do a blind test with DOC-free water. There are online manuals for using the instrument itself.

According to the EPA Method 9060A1, you need to follow these steps:

• Filter your samples through a 0.45 µm membrane filter as soon as possible after collection. This will remove any particulate organic carbon that may interfere with the analysis.
• Store your samples in clean glass or plastic bottles with tight-fitting caps. Avoid using bottles that have been previously used for organic solvents or other sources of contamination.
• Keep your samples refrigerated at four °C until analysis. Do not freeze your samples, as this may cause the formation of carbon dioxide bubbles that can affect the results.
• Analyze your samples within 28 days of collection, or preserve them by adding sulfuric acid to lower the pH to less than 2. This will prevent microbial degradation of organic carbon in the samples.
• Before analysis, bring your samples to room temperature and shake them gently to mix. Suppose you have preserved your samples with acid. In that case, you must remove the inorganic carbon (carbonate and bicarbonate) by purging them with an inert gas (such as nitrogen or helium) for at least 10 minutes. This will convert the inorganic carbon to carbon dioxide and vent it out of the sample.
• Follow the manufacturer’s instructions for operating the TOC analyzer. You may need to calibrate the instrument with standard solutions of known organic carbon concentration before running your samples. You may also need to run blanks and quality control samples to ensure the accuracy and precision of the analysis.