First, let me say that if "your boss" wants to run a specific accounting package, it's not your place to look for an alternative. It's your place, as an employee, to learn to use that software correctly. I've used QB for years, including time while working in exactly the same type of situation (pc repair and retail store). QB's worked wonderfully for us. However, we did NOT use the POS module at the retail counter. We used a full copy networked back to the accounting office. So, perhaps it's the POS module that is making your life rough.
Your post is hard to decipher, but I think I see two complaints. (1) you have to input quotes using "QB part numbers" instead of parts descriptions, and (2) creating quotes doesn't remove the parts from inventory.
(1) QB's doesn't assign the part numbers. The person doing the ordering and creating the "parts" in the inventory assigns whatever they want to assign to that particular part. Some people use bar codes, some use abreviations to describe the part and yet others use a combination of the two. If your company is using numbers that you can't decipher when creating quotes, speak to them about it. Maybe they can explain their system so that it makes more sense to you.
(2) If quotes removed the parts from inventory, your inventory would be wrong. Quotes are just that and nothing more. They are an estimate of what it would cost IF the work described WAS done. What happens if someone decides not to buy after they've seen the quote? You can NEVER use quotes to adjust inventory. Now, IF you are "installing a product" and not creating a bill for that product immediately, YOU are the one creating an imbalance of the inventory. You need to invoice the customer for anything that has been done/installed/sold to that customer and the invoice DOES remove the part from inventory immediately. You can use a quote created for that customer, IF the quote accurately discribes what you've done. You simply convert the quote to an invoice. But, if the quote isn't accurate, it should perhaps be voided (depends on what the boss wants you to do), but an invoice should be prepared immediately instead, based on what you really did do/sell.
Hope this makes sense.