Hi Romina,
I am going to have to look a little deeper as to why certain Estimates and Invoices aren't syncing over, with Currency being the possible issue. However, I can explain briefly how you can change over the Vendors in Method that you want to be listed as USD Currency.
You can Export the Vendor table, making sure to export at least the Name field, Currency, and RecordID. This can be done by going to Customize->Integration Tools, then click the "Go to Import/Export..." link. On the next screen, choose "Export a table to a file" from option 1, then choose the "Vendor" table in option 2. Choose the appropriate fields to export (using what I suggested at the beginning of this paragraph, and whatever other fields you want to see), then you go to step 5 and click the "Export to a file..." button. You can open the exported .CSV file in Microsoft Excel, and locate the "Currency" Column. For all the Vendors you want to change the currency to, change this column to the appropriate currency, for example change some from EUR to USD. Save this file, and go back to the Import/Export Menu, and choose the option to "Import into a table from a file" in step one, again choose the same "Vendor" table. For option 3, click the "Choose File" button, and locate the file you just made (and saved) the changes to. You will come to the next screen "Prepare Data", just make sure that you choose "Update existing records by matching the key fields" in Step 2, and you should be fine using the "RecordID" Column for this option. Step 3, just make sure the columns from your file match up with the columns from the Vendor Table. Now, click "Import Data" from Step 4, and this should update your Vendor records accordingly. If you have any issues with this, you can follow this article which explains how to do this in more detail.
If I require any more specific info from you regarding the first issue, I will send you an email message through the forums, but it might also help, when you get the chance, to send me an email at the adress below my signature. Make sure to let me know the CompanyAccount name you use to sign into Method with, as well as the best email address to get back to you at.
-Ben