That means if I want to study on 'Effect of environmental variable on SALAMANDER ecology', I will take plot only at the place where I find them. The place where I don't find them will not count as my plot.
it depends on what you want. At least it makes sense to investigate only sites where the species principally occurs. I would not conduct a study on elephants in Europe, just as an example.
If you only look at sites where you find the species, you might be more interested in factors you suspected to positively affect abundance or density. If you have factors in mind that might also negatively affect the species, it would be important also to include sites where the species principally should occur but actually doesn't.
Principally, it would be more adequate to sample quadrats in an area where the species principally occurs, and then look at correlations of factors within the quadrats with numbers of salamanders.
Is it a study on a community of more than one salamander species? And maybe other groups with more species as well?
You could then try a canonical correspondence analysis which visualises the correlation of several species with several environmental variables at several sites. But this is more an explorative analysis.