Jesus knew it was the Father's will for Him to be made an offering for the sins of the world. This is true because He prophesied His death and resurrection many times before. However, because of His unique relationship with God, Jesus was asking God to accomplish His will some other way, but at the same time affirming His commitment to do His Father's will and not His own.
He was not at a loss to know God's will and therefore, left this time of prayer trusting that whatever the Father deemed best for Him would happen.
He knew, when He began praying what the Father's will was and He knew at the close of His prayer, that God's will could not be accomplished any other way.
For us to pray, 'Lord, if it be thy will' in response to a promise that God has given us is nothing but unbelief and is not even remotely related to what Jesus did in the Garden of Gethsemane. One of the foundational principles of answered prayer is that we must believe that we receive when we pray (Mk. 11:24). There is no way that we can fulfill that condition if we don't know God's will in that situation. Praying, 'if it be thy will' takes us out of the active position of believing and puts us in the passive position of waiting and letting circumstances rule our lives. If we are seeking direction in an area where God's will is not already expressed through His Word, then we should pray James 1:5, and ask for wisdom. Then we can believe that we receive when we pray, and with that knowledge continue our prayer in faith.
We should not be ignorant but understand what the will of the Lord is (Eph. 5:17).
The only appropriate time to pray, 'If it be thy will' is when we are dedicating ourselves to the service of God, regardless of where or what that may be.