Which one is grammatically correct?
1.There are two steps to use this system.
2.There are two steps to using this system.
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OP's first alternative sounds completely "off" to me. In such contexts, to isn't an "infinitive verb marker" - it's a preposition that effectively means [that are] involved in1. Which simply doesn't work where the referent of the preposition is the verb phrase use this system.
The second is better, because at least using this system is a credible noun phrase (a "gerund", if you like). But personally I'd prefer...
3: There are two steps to [the] use of this system
...where the target of the preposition is more explicitly "nouny".
1 A few example utterances that might give a better picture of how to functions here...
...from which it should be clear that whatever follows to in such contexts should always be a noun.