Hi Michael,
Workbook Linking - When the Excel workbook is saved to the BOE, a reference is saved into the central management server (CMS), which holds a reference to the File Repository Server (FRS); where the file is actually stored. This indirect referencing is what is breaking your Excel File <-> Excel File linking. There may be some admin magic that you can perform on the BOE to allow Excel File <-> Excel File linking, but BOE Admin is outside of my sphere of knowledge.
Open Workbook through Browser - You should have no problems doing this. On AO versions < 1.4, you can set the registry setting LoadBehavior to start AO whenever Excel is started, allowing your users to start AO Workbooks from the Launch Pad. AO 1.4, when used in conjunction with BIP 4.1 (in Ramp Up right now), allows the use of a new, specialized, AO Info Object. When this Info Object is used, the launcher XML start methodology is invoked and AO is started with Excel.
Cheers,
Dave
