While it's possible to Open Manage | Database | relationships and change a table occurrence so that it refers to a table in another file--such as changing the invoices starter solution to pull from contacts in the contact manager, It's not a simple undertaking. The two tables are not identical and you'd have to modify the table design to handle the differences, then update layouts, scripts and possibly calculations work correctly with the new table.
As someone new to FileMaker, it's very likely that you'd find it easier to build in that component from scratch.
How to make the invoices pull up only customers and purchases bring up vendors and employee's.
This can be done, but what do you mean by "pull up" in this case? Are you pulling up records on a layout or values in a value list?
Pulling up a record. What I meant was when I am in invoices it would only pull up customers and when I am in purchases side it would only pull up vendors. I would only be using 1 contacts db. Within this db I would have a variable field that the contact record will be a customer or vendor.
I was using fm 9 which couldn't export containers and just updated to fm 11 and it can export the notes container which is very good.
I was able to copy and paste the purchase order over into the invoice, that was easy, but I have to set up the contacts to the p.o. side.
The last two items's I am still thinking of how to do:
Notes: Be able to enter a note with a recontact date to pop up. Example: John Smith's record. I need to recontact him because his application is comming due to expire.
The 2nd item is to create reoccuring inoivces and purchases. Example: ABC Company wants to purchase a widget every 30 days for 4 months. I only want to enter it once and have it automatically come up until I delete it or concludes the reoccurance frequency.
I am sure it would all have to do with script triggers, I am still pondering in my head how to write those script triggers for these last two items.
Pulling up a record. What I meant was when I am in invoices it would only pull up customers and when I am in purchases side it would only pull up vendors.
You can then have the system perform a find for all contacts fo the desired type (Customer or vendor) and look out for the possibility that a contact could be both. This possibility could be handled with a checkbox group in your contact layout.
This script would be passed a parameter: "Customer" or "Vendor". Thus it works for both cases:
Enter Find Mode  //clear pause checkbox
Set Field [Contacts::ContactTYpe ; Get ( ScriptParameter ) ]
Set Error Capture [on]
Perform Find 
You can use the on layout enter trigger to perform this script whenever you access the layout where you want to limit the contacts to one type or the other. The trigger can pass "Vendor" or "Customer" as script parameters to specify the desired contact type.
Notes: Be able to enter a note with a recontact date to pop up.
I'd use a related table of notes for this with a field for recontact dates and another number field for "Recontacted". YOu can then set up a script that performs a find for all notes records with a recontact date < Get ( CurrentDate ) and that has an empty "Recontacted" field. THis script can be set up in File OPtions to run every time you open the file. The same script can set "recontacted" to 1 to keep from popping up a reminder for it after the first time.
The 2nd item is to create reoccuring invoices and purchases.
Most invoices and purchase orders have a related lineItems table so you'd need to duplicate both the parent Invoice or PO record and also any related LineItems Records. See this thread for a script you can adapt to that purpose: Duplicating Bill Of Materials (duplicating portal line items)
The same script that checks for recontact notes can also check for invoices set up as recurring and can generate them with a version of the above mentioned script if the specified time interval has elapsed. (Invoiced record would have a "Repeat this order on" date field.)