You can set how you enter bills and pay bills in Bills category of preferences, on the Company Preferences tab.  Bills category is one of the preferences that have no option on My Preference tab:


QB Preferences Affecting Bills



Checking preferences is one of the preferences categories that has options on both My Preference and Company Preference tabs.  On the My Preference tab, there are three options on how you can use your checking accounts that are useful if you have more than one account.  However, if you only have one checking account, leave the boxes unchecked as QuickBooks will default all three options to your one and only checking account.


One of the most common errors in QuickBooks is incorrect item setup, either a mistake in the type of items or in the account assigned to items.  For example, if you only sell products or services, then you should assign Sales account to these items; but, if you sell & purchase inventory products (called inventory part in QuickBooks), you should assign the item to Sales accounts when you sell the products and to COGS (Cost of Goods Sold) accounts when you purchase them.
Some indicators on Profit & Loss report are negative revenue/expense, and understated /overstated revenue or expense.  Other indicator may be understated inventory on the Balance Sheet.  All of these are the results of the incorrect mapping of chart of accounts from your items.

To review your item list, from Main Menu > choose Lists > Item Lists, you will then open the following report by default:


One of the challenge QuickBooks users have is setting the right preferences to control the features of the program.  There are 22 preferences’ categories in QuickBooks, located on the left pane, and each has My Preferences and Company Preferences tab.  
My Preferences is used for personal options features and not every category has this tab.  Company Preferences is used for everyone in the organization.
QuickBooks accounting category control use of account numbers, classes, and closing date of your file. To view and set accounting Preferences, click Edit > Preferences, then highlight Accounting and choose Company Preferences:



One of the best kept secret shortcuts available in QuickBooks is Ctrl+Y whether you are an accountant, bookkeeper, or business owner.  What it does is giving you the behind the scenes debit and credit or transaction journal of whatever form or transaction you open.  
If you have a problem in grasping any of QuickBooks transaction, or just want to understand more of it, pressing Ctrl+Y will certainly help as it shows the exact journal of the transaction.  Let me explain more by giving you an example:
Say you are about to pay your vendor and you open the Write Cheque window from the Main Menu > banking > Write Cheques: