@Peyt , if lupus is suspected you really have to see a rheumatologist for proper testing and diagnosis.
Do you have any of the more obvious lupus (SLE) signs? Like a butterfly rash on the cheeks, lesions, hair loss, fever, painful joints etc.?
What do you mean by lupus antibodies? Do you mean AntiNuclear antibiodies (ANA)?
This can be negative in some cases of lupus. To check for lupus and other conditions a rheumatologist will probably also do the following diagnostics.
C3
C4
CBC
ESR / CRP
Anti-ds DNA
Anti-SM
Anti-RNP
ANti-SSA/SSB
ANCA (maybe also MPO3 / PR3)
Liver profile (albumin, AST/ALT etc.)
Urine analysis