Line intercept transect (LIT) or point intercept transect (PIT) surveys are applied to estimate the percent cover of sessile species such as corals, sponges or encrusting bryozoans. In these methods a transect line is laid over the bottom (usually coral or rocky reef). In LIT the length of line overlying various kinds of organisms is then measured (usually with an accuracy of 1 cm), either by graduations on the transect line or by a hand-held meter tape or stick. Some researchers have used chain (chain transects) instead of transect line, counting the number of chain links overlying each kind of substrate instead of measuring distance of coverage. Chain transects is the only method that provides information on substrate rugosity. However, it can damage fragile and fan shaped or branching organisms and should be avoided in such cases. In PIT, the line is marked at fixed points and sessile benthic organisms or substrate categories directly beneath the marks are recorded. LIP and PIT methods tend to be quicker than plot sampling methods; in comparison to quadrats they are less sensitive to small scale spatial variation. PIT is much faster than LIP and appears to be more time- and cost-efficient, which is important when there are field time limitations. LIT, in addition to percent cover, can provide population densities as number of individual colonies per unit area.
You may find some useful information on these techniques and on quadrat sampling in the following publication: Katsanevakis et al., 2012. Monitoring marine populations and communities: methods dealing with imperfect detectability. Aquatic Biology 16:31-52.
https://www.researchgate.net/publication/230730079_Monitoring_marine_populations_and_communities_methods_dealing_with_imperfect_detectability
Article Monitoring marine populations and communities: review of met...
It depends on what you are measuring, I can help a bit on belt transects, take for eg. a 50m x 8m transect, lay out your 50m transect tape, estimate 4m on each side and move along the tape checking for your organism of study. quadrats, with seagrass its usually 30cm x 30cm, 50 cm x 50 cm, 1m x 1m or 2m x 2m.
I hope i helped!
More than using those methods you mentioned, maybe you should try point intercept transect (PIT) instead. Just recently, Roberts et al. (2016) conducted an experiment on coral reef species richness. It showed that point intercept transect (PIT) being the most efficient method for coral survey. Maybe that is the best way for your study. :)
In his study's abstract, he said that "PCT provides a more accurate estimate of local-scale species richness than the LIT, and is an efficient alternative method for surveying reef corals to address questions associated with alpha-diversity, and rare or incidental events."
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152335
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