The purpose of the Serial-to-I2C app is to receive commands from a serial interface and translate them into I2C operations (and return the I2C slave's response over the serial interface). For example, receiving the 'S' command on the serial interface tells the Wixel to generate a start condition on the I2C interface, so the commands you wrote above are all sequences that you should be sending to the Wixel serially.
The reason I recommended on the phone that you use the serial transmitter utility is that you need to send some of the bytes as raw values. To send
'S', 0xA6, 2, 0x2E, 0x00, 'P'
you should not be sending a single quote, S, single quote, comma, space, 0, x, A, 6, and so on (you seem to have figured out at least part of this already). Instead, you should be sending the character S (i.e. a byte with value 0x53), then a byte with value 0xA6, a byte with value 2, a byte with value 0x2E, etc. Not many terminal programs allow you to send raw bytes this way, but it looks like you can do it in Br@y Terminal by prefacing a hexadecimal value with a '$', like this:
(You might also want to select the "HEX" radio button in the Receive section of the Br@y Terminal window so you can see the responses from the Wixel in hex format.)
Either sending the two commands separately or joining them together on one line (keeping the stop and start between the two commands) should work. However, the last sequence you wrote (removing the stop and start between the two commands) would probably not work, because most I2C devices use those start and stop conditions to separate different commands. I recommend that you check the datasheet of your accelerometer to make sure the format of your I2C commands matches what it expects.
If you want to write an app for the Wixel to send these commands directly (instead of using the Serial-to-I2C app to translate serial commands to I2C), you should look at the SDK documentation for i2c.h, which describes the functions in the i2c library that you can use in your app.