"Plugging in X" vs. "plugging X in"
Solution 1:
A combination of your two examples would be correct:
Plugging that value into the previous equation..
In this sentence you are dealing with the phrasal verb 'plug in', which has then been split by the noun ('that value').
Solution 2:
Either "Plug in that value" or "plug that value into" are fine depending on the rest of the sentence, but not "Plug in that value into".