It may be depended on the lizard species to some extent. As example, for rock lizards you can see paper:

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2010.01498.x/abstract

I agree with Levan. It depends on the species. I would suggest you search the literature on the species that you are interested, and from there you can develop an experimental set up. You would also have to determine your research question. Are you interested in one specific species, or do you want to find out how many different species are in your study area? Home range, or occupancy, or population size? What habitat are they found in (on rocks, in trees, forest ground, grasslands, wetlands etc?) . What size are your lizards? If you provide us with more specific information, we might be able to suggest a few methods, ideas, papers.

Thank you very much Levan and Konstanze. I am interested in finding out how many species are found in an area and how these species are able to co-exist. Also use these as indicators of habitat condition. Here in Cavite, Philippines I have documented 30 species of lizards and I have started to observed patterns in relation to species distribution. I also like to incorporate occupancy estimates as influenced by habitat covariables and may be use species or species assemblages to assess environmental conditions. Again thank you for taking the time helping me.

Species co-existence: co-existence is possible through specialization, so where are the differences in your species? can you group them? Day-night activity (temporal avoidance, searching for temporal patterns in activity), food-specialization (what food is available in what habitat type, herbivores vs insectivores vs omnivores etc, insect diversity, food item sizes....), spatial avoidance (living in trees, on rocks, in shrubs etc).....

Habitat condition: That's a tricky one, first you would have to define what is a good condition and a bad condition. Diversity is not necessary the key when you look at 'natural' systems, which can have a natural low diversity. I would concentrate here on species (single or groups) that are very specialized and react to small changes in the environment. E.g. the spotted owl (USA) example, they need old growth forest for breeding , they disappeared from forests which were subjected to intensive timber harvest which removed all old growth (that's a simplification of the problem, but you get the idea).

Occupancy estimates vs habitat covariables: There is a large amount of literature on occupancy studies, and every method has its pros and cons, mostly, I think, along a gradient from data-hungry, very detailed analyses to faster, not so expensive approaches.

I integrated incomplete detectability of the species in my analysis of habitat characteristics that affect occupancy of a rock-dwelling lizard species, using the statistical analysis developed by D. MacKenzie et al (eg. MacKenzie et al. 2002 'Estimating site occupancy rates when detection probabilities are less than one' Ecology). However, there a limitation, possibly on the amount of data that you can integrate.... I think in general presence absence data is superior to presence only data, because the information of the habitat where the species is absent is integrated in the analysis. Maybe this paper could be interesting: Leathwick et al 2006. Variation in demersal fish species richness in the oceans surrounding New Zealand: an analysis using boosted regression trees.

Hopefully some of this helps!