I have determined how to upload custom mining software however is there a way I can add the mining software as an entirely new entry is the list under profit profile properties?
Yes, you need to add the uploaded custom mining software to the Managed Software section in AM. After doing so, you'll see it listed under the profit profile properties.
Also, can I set miner specific entries like, -i 25,for certain algorithms (or possibly custom pools) and not for the entire miner software? I have noticed I can tune some algorithms up a bit more but then it causes crashing on others.
There's multiple places to add additional commands. Where you add them depends on where you want to apply it. The simplest is adding the
-i 25 at the Custom Pool level. But this may not work if you have rigs that need different intensities... so you can add it at the rig level. You can even add it at the online services pool level.