Please consider taking a professional on-site HPLC maintenance class that is specific to your exact model of HPLC system. This is the fastest and best way to learn the correct maintenance procedures for YOUR HPLC system. Consider taking some hands-on formal classes to learn the fundamentals of HPLC as they apply to YOUR HPLC instrument and software to. It takes most users many years just to learn the basics and taking hands-on professional classes can help you understand and apply these concepts more efficiently while you are learning. Please have a more experienced chromatographer help you.
(1) The correct degasser priming/flushing process
depends on the exact model of HPLC degasser you have (which you did not provide). When flushing or priming ANY HPLC vacuum degasser (you can use the pump or a syringe), you must first know what the internal channel volume is for that degasser model (plus the tubing volume). Example: For the G1322A, channel volume is between 10 and 13 mLs/channel, each. For the G1379A/B it is 1 mL/channel. To flush ONE channel you need to rinse through it enough liquid to fill and flush it 2 or 3 times, plus the volume of low pressure tubing. So for a G1322A, flush about 30 mLs of liquid through each of the 4 channels when you fill it with mobile phase, change mobile phase bottles or begin to use it after a weekend. Flush about 10-12 mLs through each channel of the G1379A/B series. Please do this for ALL 4 channels, even if you do not plan on using them all. All channels must be filled with liquid at all times. Do not plug an unused channel, the liquid will quickly evaporate inside. Air inside a channel will stress the vacuum system (leading to early failure). Connect unused channels in-series with other channels to keep the 'wet'. Never leave water or buffer sitting in a channel. Critters will grow in it and contaminate your flow path.
(2) Buffers: Any buffers used with your HPLC system (that includes phosphate buffer) should be routinely flushed from the system with high purity water (not IPA). Two types of flushes are used. The column should be flushed with an appropriate solution after use each day (do not store the column in buffer or pure water). The rest of the HPLC flow path must be flushed down to remove buffer. The idea is to flush out the buffer so salt crystals do not form. For RP, start by flushing with pure water, then switch to water mixed with some organic (e.g. MeOH/Water 60/40) to stop corrosion and prevent bacterial, algae or mold growth.
(3) Column cleaning. Basically, first, refer to the column manufacturer's recommendations about what can and what can NOT be used to flush through the column (also, any pressure, pH or temp limits). Next, you flush the column with whatever solution is safe to dissolve one hundred percent of whatever is dissolved or fouling the support. You want to flush any retained material off, w/o damaging the support. The best solution to do this is going to be different for each application and person. IGNORE any suggestions by others of using some 'universal' flushing solution. Any universal washing solution would not address your own applications or use. We have a scientific way of doing things and it starts with information first. What types of samples were run through the column? What solvent is stronger than my mobile phase and will dissolve them 100% to remove them (w/o damage)? Now you have the answer.
(4) The PTFE frit should be changed EVERY MONTH. It is a $5 filter (cheap) and designed to catch normal piston seal debris plus any large particles that might sneak into the system. Normally, it is snow white in color. It is cheap insurance to protect the flow path. Don't forget to change those bottle frits too.
If you are in the USA, please consider my employers professional Agilent specific HPLC training classes. They have taught more than 10K scientists expert techniques and methods to use and service these system over almost 30 years. More info here:
http://www.chiralizer.com/hplc-products---training-classes.html