You need to take the time and delay of your C-Gear seed and work backwards to find your Standard Seed.
1) Before you attempt this, move all Entralink Pokemon except your target into the Deep Clearing. This minimizes the effect of randomly moving Pokemon on your timing.
2) Let's say I have a C-Gear seed with a date of 2\14\2012, a time of 3:59:57 and a delay of 5623. Each delay is 1\60 of a second, so we need to divide it by 60 to get the total number of seconds. 5623 / 60 = 93.7 seconds.
3) Subtract 93.7 seconds from my C-Gear seed time to get the time of the standard seed, because that's when delay starts counting. 3:59:57 - 93.7 seconds = 3:58:23
4) Plug the date, time, and your DS parameters into the Adjacent Seed tool (under the 5th Gen Tools menu), and click Generate. You'll be given a list of standard seeds. Seeds in white have your target seconds; seeds in grey are adjacent seconds and\or Timer0s. The tool will also give you Chatot pitches for each seed so you can verify your seed.
5) Plug the seed in the main window, with Gen 5 PIDRNG and Entralink Pokémon selected. Calculate the initial PIDRNG frame. Look for a frame that has the nature you want, but also gives you enough time to get into the Entralink. (50 seconds minimum is ideal.) It also should not be on a "skip" frame.
6) When doing your Chatters to verify your seed, you must do them in a multiples of 3, otherwise the timing and skipped frames will change.
7) When you turn on the C-Gear, that is when you must start keeping track of time. Enter the Entralink when necessary.
8) Move to the forest as quickly as possible and then talk to the Pokemon to stop it from moving. Wait until the timer says you have reached your target frame, then select "Yes" to encounter your Pokemon. If you were successful, your Pokemon should have your desired nature. If not, the moving Pokemon's advancements may have messed up your frame.