Here's my exact method after a lot of trial and error (and recommendations by members on here):
-in a small clean glass add 1/4 cup warm water (~100-105F)
-place appropriate amount of yeast (1/4-1/2 tsp)
-add in a pinch of sugar
-mix well trying to get it to froth a bit, every minute or so I'll quickly beat the water like making scrambled eggs
-boil ~2 cups of water in a clean pot
-put the cap of your bottle in the water
-CAREFULLY pour the boiling water into the 2L bottle
-put the cap on and gently roll the bottle so the scalding water sterilizes all surfaces (please be extremely careful with the steam which will burn you on contact)
-add 1 1/4 cup common white sugar
-add a tablespoon of protein suppliment (I use old baby formula powder, a single container goes a LONGGGGGGGGGG way)
-mix for 20-30sec with gentle swirling (most of the sugar will dissolve because the water is so hot)
-fill 2L bottle with cold tap water to about 3/4 full while swirling
-the water temp in the bottle will now be about 100-110F which is perfect
-pour in the yeast mixture which has been sitting for about 10 minutes (and stirred every minute or so)
-gently swirl the 2L bottle so the yeast and sugar are evenly mixed together
Now (and this is very important), depending on the temperature of the room you may want to wait 30min or so before reconnecting the bottle to the tank. When hot things cool they contract. In your 2L bottle that means it will start to pull a vacuum (why the water gets sucked into the line). If you wait 30min or so the CO2 production from the yeast will pressurize the bottle against the vacuum and you won't get liquid sucked into the line.
Some final quick points:
-The time period with the yeast in the small cup is VITAL to the survival and production of the yeast. Do not skimp on this step. From start to finish it takes me a little more then 10 minutes.
-don't use baking soda (to buffer pH), the sodium in it is poisonous to the yeast, and yeast are well adapted to thriving in low pH conditions
-boiling of the water and then adding to the bottle will sterilize and kill most of the bacteria in the bottle. Bacteria will out-compete your yeast and cause a loss of production (or more likely a shorter production time, ie 10 days instead of 14). The boiling process will also remove most of the chlorine from the water, lowering the total chlorine amount when you add the yeast in.
-More then 1 cup of sugar (~10%) is toxic to the yeast. All you are really doing is wasting sugar, since yeast go dormant/die when alcohol levels go above 10% (for most common baker's yeast). If you are using more expensive wine/champagne yeast you can use more sugar.
-The protein powder (baby formula) is a trace nutrient supplier that will extend the life of the yeast and thus its production of CO2. Sugar provides the fuel source, but just like plants (and nitrogen), yeast require more than that to survive and thrive.
-You have a 29 gallon tank. I would recommend 2 2L bottles staggered a week apart (I do this with my 20 gallon setup). This will help to prevent BBA which is generally caused by fluctuating CO2 levels. By changing out a bottle each week (14days per bottle), you will have a much more consistent level of CO2. Another benefit is the virtual elimination of the vacuum effect in a 2-stage system since the new bottle is being pressurized by the old bottle. The CO2 might slow or stop from entering the tank but it should not back up into the tubing.
-Note that I use between 1/4 and 1/2 tsp of yeast (1/4 during summer months, and 1/2 during winter months). Many other recipes that call for more is because they are killing off a significant portion of the yeast due to improper practices (ie adding to cold water with no oxygen, baking soda, bacterial contamination, etc.)
HTH