I have a Focurite 18i20 and I am getting a lot of clipping when I plug my Ibanez RG 7 string guitar in direct. I use the pad button and the instrument button. Still, no matter how much I turn down the gain knob on the Focusrite I still get clipping. I have a DI box and saw that as a suggestion.
Now, when I turn down the fader in Sonar it stops the clipping.
Could it be that I am using an instrument cable that only has one pole? Would a cable with two poles fix the problem?
I mention it because the Focusrite manual mentions it.

I think your Focusrite might use the same pre amps and mix control my 6i6 uses. 
First, If this is an electric guitar you really are better off using a DI. 
I find the pre amps are not very good at electric guitar or bass so I use other options for those. And yes they will clip because they are overly sensitive IMHO. 
So if you have a DI use that and the XLR input. 
Electric guitars give the best tone when they are connected to a guitar amp or guitar pre amp. You'll get a thin sound when using the instrument input. 
The instrument input works fine with acoustic electrics and active basses which both have pre amps. 
 
Your reference to a cable is instrument cables are Tip/Sleeve or TS and are not balanced. This is the correct cable for a guitar or bass and most keyboards. Balanced cables are Tip/ring/sleeve  TRS and are used for longer cable runs between balanced equipment, like a mixer or powered speakers. TRS and XLR are more or less the same balanced cable, just different connections.
 
Your DI box will convert your hi impedance guitar output into a Low Impedance balanced signal. But depending on the DI you will always be better off either miking a amp, or sometimes the using the amps line out or a good quality guitar pre amp like a Sans Amp. 
Radial DI's are the exception. 
 
I have used the Combi jack set to instrument in Mix Control for bass and guitar in a pinch, but you have to play very smooth and evenly, or put at least a compressor pedal ahead of it. I'm not a fan of the Focusrite pre amps for this very reason. I do not have this issue when using my Tascam. 
 

Using DI you want to use Line in on the router (in Mix Control you actually need to click and hold the option to see the 3 items on that list).

Also on the Mix Control, it is best to choose the FX option for that input. It will route the processed signal to the DAW and you can set the compressor like a limiter, set ratio way high, and also the threshold high (like -5 to -10dB). That is only to catch errant spikes and prevent clipping, do not run too hot going in (let the gain reduction meter guide you, it should be subtle and intermittent).
 
Edit: I did a quick check of my settings, and my threshold is -12dB and ratio is 5.4:1.

Thanks for the help guys - much appreciated. I have a cheap Rolls Matchbox DB25 DI box I will try. And I didn't evn think about changing anything in the Mix Control. See - over a year now with SPLAT as my first DAW and I am still learning things and making rookie mistakes.

 And I didn't evn think about changing anything in the Mix Control. 
 
But your interface has the  pads/ line / instrument toggles on the front panel so I would only assume they are redundant in mix control or possibly your version of mix control should be without those toggles in the GUI. 
If it does have both that's sort of confusing. or possibly the GUI mirrors the hardware settings. 
 
The Rolls DI is not really of the caliber to make any difference.  
 
 

Cactus Music
 The Rolls DI is not really of the caliber to make any difference.  

I did not think it would be - I have not even tried using it. I bought it years ago and used it for bass guitar for live performances.

The Mix Control software is definitely a good thing to learn. It can be confusing at first, but once you know your way around it, it is useful. One of the best introductory videos is here (15 minutes).
 
I have also found that when working with a DAW, it is best to leave Mix Control open, even if minimized. I have noticed weird behavior if it is not actually open, so popping it open after the interface is turned on seems to keep things in order.

I have also found that when working with a DAW, it is best to leave Mix Control open, even if minimized. I have noticed weird behavior if it is not actually open, so popping it open after the interface is turned on seems to keep things in order.
 
At first I actually though you had to have it running but since found unless you need to make a change this is not so. So myself I only open it to toggle the PAD/Line switches. I leave my buffer at 7ms which seems to cover all modes of what I do. 
At first I learned all the monitoring settings and found it pretty cool, but I did not like having to keep the screen open on my second monitor while I worked. So now I use a small mixer for headphone balance.