Popular method used for benthic lifeform survey  is by English et al. 1997,,Line Intersect Transect (LIT) method: include size, species, density, age estimate, sex, and distribution (if applicable) depending on your study objectives. However, LIT has evolved, for example aided by underwater camera, etc. You may choose which ever is suitable to your logistics not undermining the validity of your results.

You can look at several population parameters such as growth, mortality and recruitment patterns. Using FiSAT program is one of the popular methods. You can access this in the internet. It's a freeware. 

We use a grid-plus based sampling design for benthos in the Wadden Sea. I attached the publication. Depending on your question/effort you can increase or decrease the grid size. For looking at growth, mortality and recruitment patterns etc. you need to keep it up for several years.

Good luck!

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