Thank you Ajeh for your help. I think I came up with a easier solution to my issues. The main issue I was having is that USPS and UPS were giving shipping options on everything.... no matter if they qualified for free shipping or if it was weights way over the two company's limits.
My difficulties were that I wanted to offer free shipping with a minimum order of $40 for all "non-freight" items. However I was not able to set all the parameters (with my limited knowledge) to limit shipping offers if they were not included with shipping discounts, etc.
What I ended up doing is turning off UPS and USPS shipping modules. I added the "Shipping by Quote" and turned on "table".
I decided to estimate a shipping charge per level of cart price and simply charge a set amount per level (table), this way I could manage my free shipping by cost as well as limit free shipping by cost (the freight that does not qualify for free shipping is well over $300)... so my table settings read:
9.99:6.99,19.99:7.99,29.99:8.99,39.99:10.99,299.99:0.00,4000.00:750.00
This translates to "if the cart order value is "X"/then the shipping charge is "Y"
0.01 - 9.99 = $6.99 shipping
10.00-19.99 = $7.99 shipping
20.00-29.99 = $8.99 shipping
30.00-39.99 = $10.99 shipping
40.00-299.99= $0.00 shipping
300.00-4000.00 = $750.00 shipping
I had to put in a dollar amount range to cut off the free shipping, so I estimated that I would not receive a single order over the cost of $300. If that starts to happen all I have to do is edit that parameter. I had to also put a shipping cost high enough to equal to a price over the actual freight costs that would occur so I would not be held accountable to honoring a automatic freight quote.
I added Freightquote.com so the clients could get an estimated freight cost in the shipping calculator... however I added the "Shipping by Quote" so the customer can either submit the order for a freight quote, or call us for the quote... then they can manually enter the quote and check out. I also added, "Orders over $300.00 and freight orders will require customers to use "Shipping by Quote" for the best discounts." in definitions.
This cleaned up my shipping page and put me in control of both my free shipping and my freight orders. As well, I don't have to show UPS and USPS. We have control to ship either way without the customer forcing us to use one or the other.
Hope this may help others trying to deal with this issue and not really advanced in coding.