Clove hitches are still the most popular knots used in models. If the model is very small, sometimes the ratlines can be passed though the shroud using a needle. Because thread defies gravity and the tension is far higher in scale models than real rope at full scale, watered down PVA is commonly used to freeze the lines in the desired, downward hanging loops, and also to prevent the clove hitches from coming loose.
There are many methods for ensuring that the ratlines come out as nice, even and level rows at equal distance apart from one another. Many use a white cardboard background with regular horizontal lines on it, inserted behind the shrouds while tying ratlines.
I use a wooden alignment jig that clamps onto the shroud and fits precisely between rows of ratlines. It has 300 grit sandpaper glued to the inside surfaces so once clamped onto the shrouds, it won't shift. I found that when tightening each clove hitch, you pull the thread away from the shroud straight toward you with a light tug while holding the shroud with needle pliers just above the knot, with the spacing tool just below the knot, then tug the line in a direction parallel with the ratline, in the direction you are working. The knot is small and tight. I tighten each knot as I go, and then slide them up or down on the shroud if they need straightening. The spacing tool makes sure that the row is mostly in the correct angle, but properly spaced between rows, so few adjustments are necessary. Every three rows, I check the height and location of the ratline to the channel, and compare that measurement to the ratline on the opposite side of the ship, so they line up. Use of the spacing tool made these measurements usually come within 1mm from port to starboard, so adjustments are quite small to match the ratlines. It's good to apply the thinned PVA glue to each row before making the next one, so none of your finished knots get loose. It took me about 200 knots to get a system down.
Below is the alignment jig in use, using clamps, before the jig was modified to use wire staples, making it much lighter and easier to use.
