If you are sophisticated enough in Excel you can try to work with the Consolidation feature which is under "Data", "Consolidate". It will allow you to specify which is the column or row of labels you intend to use that will be matched between the two files. Attached is the help information supplied by Excel on how to do it:
Guidelines for specifying source areas for a consolidation
When you consolidate data, you specify the source areas of the data either in 3-D formulas or in the Reference box of the Consolidate dialog box (Data menu, Consolidate command). The source areas can be cell ranges on the same worksheet as the consolidation table, on different worksheets in the same workbook, or in different workbooks or Lotus 1-2-3 files.
Before you begin
Name your source areas To make source areas easy to keep track of, name each range and use the names in the Reference box.
Referring to source areas
On the same worksheet When the source areas and destination area are on the same worksheet, use cell or range references or names.
On different worksheets When the sources and destination are on different worksheets, use sheet and cell or range references or names. For example, to include a range named Budget from the Marketing worksheet in a consolidation on the Summary worksheet, enter Marketing!Budget.
In different workbooks When the sources and destination are in different workbooks, use book, sheet, and cell or range references or names. For example, to include a range named Sales from the Eastern Region worksheet in the 1996 workbook in the same folder, enter the following:
'[1996.xls]Eastern Region'!Sales
In different storage locations When the sources and destination are in different workbooks in different locations, use the full path, book, sheet, and cell or range references or names. For example, to include a range named Revenue from the February worksheet in the Sales Department workbook in the Budget Worksheets folder, enter the following:
'[C:\Budget Worksheets\Sales Department.xls]February'!Revenue
Note You can omit the sheet names from the references if your workbook has names that you assigned, rather than labels used as names by Microsoft Excel. For example, '[1996.xls]'!Sales or '[C:\Budget Worksheets\Sales Department.xls]'!Revenue.
Tip To enter a source reference without typing, click in the Reference box, and then select the source area. To select a source area in another workbook, click Browse. To clear the Consolidate dialog box out of the way temporarily while you select the source area, click Collapse Dialog .
Consolidate data by using 3-D references
On the consolidation worksheet, copy or enter the labels you want for the consolidated data.
Click a cell that you want to contain consolidated data.
Type a formula that includes references to the source cells on each worksheet that contains data you want to consolidate.
Repeat steps 2 and 3 for each cell where you want to consolidate data.
Tip To enter a reference in a formula without typing, enter the formula up to the point where you need the reference, and then click the cell on the worksheet. If the cell is on another worksheet, first click the worksheet tab, and then click the cell.
Consolidate data by position
Click the upper-left cell of the destination area for the consolidated data.
On the Data menu, click Consolidate.
In the Function box, click the summary function you want Microsoft Excel to use to consolidate the data.
In the Reference box, enter a source area you want to consolidate.
Click Add.
Repeat steps 4 and 5 for each source area to consolidate.
To update the consolidation table automatically when the source data changes, select the Create links to source data check box.
To create links, the source and destination areas must be on different worksheets. Once you create links, you cannot add new source areas or change the source areas that are included in the consolidation.
Note When you consolidate by position, Microsoft Excel does not copy the category labels in the source areas to the destination area. If you want labels for the destination worksheet, copy them or enter them manually
Consolidate data by category
Click the upper-left cell of the destination area for the consolidated data.
On the Data menu, click Consolidate.
In the Function box, click the summary function you want Microsoft Excel to use to consolidate the data.
In the Reference box, enter a source area you want to consolidate. Make sure to include the data labels in the selection.
Click Add.
Repeat steps 4 and 5 for each source area you want to consolidate.
Under Use labels in, select the check boxes that indicate where the labels are located in the source area: either the top row, the left column, or both.
To update the consolidation table automatically when the source data changes, select the Create links to source data check box.
To create links, the source and destination areas must be on different worksheets. Once you create links, you cannot add new source areas or change the source areas that are included in the consolidation.
Note Labels in a source area that do not match any labels in the other source areas result in separate rows or columns when you consolidate data.