Your substitutions should be at the correct amounts for your level. However, you can always check one or two meals just to be sure.
Many people choose to do ALL their meal planning on their own and don't use the Sample Menus at all. Some use the Samples as a pattern for how to distribute calories and fat throughout the day; then they substitute similar types of foods that are easier to prepare, or less expensive or whatever.
Some folks also use the Exchanges to plan their meals. The Exchanges are listed in Section 5 of the Healthy Eating Guide. They're groups of foods that have relatively the same amount of calories and fat. If this appeals to you, there's a chart on p. 20 of the Healthy Eating Guide that lists the number of Exchanges from each group -- at each alli calorie level.
There's really a lot of flexibility with the alli Program. For those who like a lot of structure there's the Sample Menus, for those who want to do the planning they're welcome to do it on their own.
Please let me know if you need anything else.
Pat Baird, MA, RD, registered dietitian