Yeah, if they have been fairly submerged for a couple of days now then be prepared to endure a poor germ rate. Not saying it's definite or anything, but likely.
I'll tell you how I do it. This may not fit your needs, but it works pretty well for me.
I sacrify my seed in a pill bottle lined with sand paper. I scuff them real good. This allows the water to readily penetrate the seed
I soak them in pure water in a shot glass placed in a warm, dark spot. You will find a general consensus to not allow them to soak more than 24 hours. I stick to this advice religiously.
I fold up a couple of paper towels, wet them with pure water and put them on a plate. Then I dump the shot glass into the paper towel and fold it over so the seed is covered. Then I set the plate on a slight angle so the excess water pools on the lowest side. I'll let that set that way for a few minutes. This will usually leave the towel at a perfect moisture level.
After the excess water has drained out I poor it off, cover that plate with another plate (making a "UFO" shape) and set over the ballast of my flos. This seems to give it that 'perfect germ temp'. I usually see root tips within the first 24 to 48 hours from start.
Hope that helps bro. But there are a few ways to get this done. As long as you listen to what old WALT (Water, Air, Light, Temperature) is tellin' ya, it's all good.
