There are a few options that you can play with from the Advanced Options window. To access the Advanced Options window, right-click a button and choose Advanced Options....
Positioning your buttons
You may adjust the position of your button on a horizontal line which starts at the bottom of the phone field it is tied to. Under Button positioning, you may enter a number of pixels. That's the number of pixels between the right edge of the field and the left edge of the field. By default, it is set to 2, which means that the button lies 2 pixels to the right of the field.
Here is what it looks like when set to 2 pixels:
If you set the value to a negative value, the buttons will appear on top of the phone field. Here is what it looks like when set to -43 pixels:
Opening the New History window to record the result of your call
By default, The Skype Plugin for ACT! opens up the New History window shortly after dialing. If you do not want the window to open automatically, uncheck the checkbox under Record History. If you want to adjust the delay after which the window is open (3 seconds by default) you may do so under Delays.