For example, I would like to have a level of Roman numerals, followed by capital letters at the next level, followed by Arabic numerals. Word decides to put lowercase letters and then Arabic numerals. I also prefer to use parentheses, but Word automatically puts periods after the letters/numerals.
If I understand you right, you should be able to fix this problem by customizing the outline numbering in the template attached to the document:
Choose Format » Bullets and Numbering, and then click the Outline Numbered tab.
Click the outline format closest to your needs, click the Customize button to display the Customize Outline Numbered List dialog box, and then click the More button to display the full dialog box (see Figure 4-9).
In the Level list, select the level of outline numbering that you want to customize, and then use the other controls in the dialog box to apply the numbering and formatting you want. Repeat the process for the other levels of the list that you want to change.