Which one is grammatically correct?
1.There are two steps to use this system.
2.There are two steps to using this system.
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.
Both are correct in two senses but it depends on the people from different nations. In my opinion almost every ESL learners select the first one at once. But a native may easily select the second one ..