It depends on if you're getting data unique to a sampling type. We use both methods and get the same species, but we do get different sizes using different methods. So it depends on what you're looking at. We DO get different species and different sizes with backpack electroshocking vs. boat electroshocking.
What is your total sample size? For a single season's worth of data we're sampling over 10,000 fish electroshocking. Our gillnets are much less effective, but we're doing short soaks to minimize mortality. Gillnet mortality is obviously much higher than electroshocking. We see between a 1-2% mortality rate electroshocking. Frankly, I hate gillnets and am glad we're done using them.